Spycraft wins, hands down, no contest, IMHO. The only things you can do with D20M out-of-th-box that you can't do with Spycraft out-of-the-box can be done as well or better by using Spycraft+D&D than by using D20M.
However, in the interest of being a bit more useful, let me make some specific breakdowns:
Action Dice (Spycraft) vs. Action Points (D20M)
You get 1-3d6 Action Points per level. Each use either adds d6 to a d20 roll, or lets you use an ability you otherwise can't use. The don't replenish/regenerate. IOW, you get (on average) 4-11 Action Points per level, and when you use them, they're gone. That's less than one Action Point per average encounter. As an additive to a die roll, they're fairly pointless (too little effect), especially at higher levels. As a necessary expenditure to use one of your nifty abilities, they're too powerful--and thus too rare. You're either gonna never use them, hording them for something more important ('cause you never know what might be around the next corner), or you're gonna run out frequently. They become not a cool player-influence mechanic to allow heroic stunts, but instead become just another resource to manage, like spell slots and hit points.
You get from 3 d4s to 6 d10s for Action Dice, depending on level (non-cumulative). That's how many dice you get per session. They replenish each session, but don't roll over. You can also get Action Dice awarded by the GM for--well, for whatever. Presumably for exceptional RPing or a very good plan, or the like. Each use of an Action Die either involves rolling it and adding it to a d20 roll (and you can roll multiple Action Dice to add to a single roll, and do it one at a time), or spending it to activate a critical success or fumble, or increase your Defense total for a round. You can also use them to call for Favor and Inspiration checks. These are essentially metagame mechanisms that let you get a little boost when you really need it--either help from an in-game source, or a hint from the GM. This, combined with the crit/fumble mechanism (all skills, not just combat, have a threat range, and an error range: turning a threat into a crit involves spending an action die, rather than random chance, and turning an error (presumably an enemy's error) into a fumble is also something you choose to do) really add something cool to D20: genuine player input to the game, so that you can have some control, guaranteeing cool heroic stunts when they are cool, and not having to suffer through crappy rolls mucking up the final confrontation, after having critted every kobold you slaughtered. Of course, you don't have complete control, just some influence--it wouldn't be fun/challenging if you hade complete control--but you have enough to be worthwhile. The replenishing nature of Action Dice, combined with their genuine effectiveness, makes them very useful, without unbalancing the game at all.
Advantage: Spycraft
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FX (D20M) vs superscience (Spycraft)
D20M has something called an FX system. If you're familiar with other [semi-]generic systems, you'll be expecting a framework system that will let you do whatever extraordinary stuff you want to in your game--spellslinging, super-science, occultism, psychic powers, alien tech--whatever. This isn't it. It's a stripped-down version of the spell, psionics, and magic-item systems from D&D3E. Yes, you can use it for other things, by assigning spell equivalents to whatever it is you're describing. But it suffers from the same limitation as D&D magic in general--there's not much of a framework for extending it. If there's a spell that's pretty close to the effect you want, no problem. But if you want to do something completely different, you're only about one step better than guessing when it comes to assigning it an appropriate level. Furthermore, it is almost identical to the relevant systems from D&D3E. So, if you want to incorporate D&D-style magic, psionics, or magic items into your game, you can end up with almost exactly the same results just by opening up your PH/PsiH/DMG. D20M gives you essentially nothing new in this area.
Spycraft doesn't have a general FX-type system. Instead, it has broad-strokes rules for super-science. It gives good, easily-applicable general guidelines for what considering something super-science does, such as increasing DCs to analyze or detect. And it ties in strongly to the skill system and feats/class abilities, rather than being an almost-wholly-separate thing, as the FX system in D20M is.
Advantage: Spycraft. If what you see of the FX system looks superior to you, use your D&D books with Spycraft, and you'll still be doing better.
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Psionics
Spycraft doesn't have psionics in the core rules. You have to get the Shadowforce Archer campaign setting to get them. That said, if you want psychic powers in your game, it's a steal. The psionics rules in D20M are, as i've said, pretty much a clone of those in the PsiH. Which means that they are pretty much a clone of the spellcasting rules in D&D3E. I.e., not very much like psychic powers as depicted in most modern fantasy settings (Carrie, Scanners, Babylon 5, Star Trek, Star Wars, X-Files, Minority Report, etc.). The only genre i can think of that depicts psychic powers that behave anything like those in D&D3E (and therefore D20M) is DragonBall Z, and other anime fighting stories.
In contrast, the psionics system in Shadowforce Archer rocks--it has the feel of psychic powers, and mechanically ties in sensibly. You can relatively easily do things like scan minds and fool people, it's harder to physically affect the world, and you won't be summoning matter out of nowhere.
Advantage: Spycraft. Even if you take into consideration the fact that it doesn't have a psionics system in the core book, you can always mate your D&D materials to Spycraft, and have everything that D20M does on psychic powers.
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Equipment
D20M has a lack-luster equipment list. It pretty well covers those real-world items that "adventurer" sorts might want. And that's about it. The magic items section in FX is the only place that includes unusual stuff. And, again, that suffers from the list approach of magic items in D&D.
Spycraft covers all the real-world stuff, and all the cutting-edge stuff, and a whole bunch of over-the-top stuff, a la James Bond and Mission Impossible. And it's easy to tailor the equipment list for your campaign style: frex, you could just cut out anything with the "superscience" descriptor, and you'd instantly switch from James Bond/Avengers to Die Hard (or maybe Mission Impossible).
Advantage: Spycraft. no contest. Just reading through the Spycraft equipment chapter makes me want to play a game, and i don't even like the genre. Oh, and i forgot to mention the very cool systems for hacking and computers.
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martial arts
The D20M system has about as much flavor as monks in D&D--it's all about results, and in the process completely skips over any flavor.
The system in Spycraft is also results-oriented, but has a nice veneer of flavor to go with it.
Advantage: Spycraft, but only by a hair. See the Feats section, below, for more related commentary.
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classes
Spycraft follows basically the D&D model, except with classes that are appropriate to the action/spy genre, rather than high fantasy. Only a couple of really notable changes here: The biggest of these is to multiclassing. You no longer pay an XP penalty for multiclassing. However, each class has a "core ability", and you only get the core ability if your 1st level in the class is also your 1st character level. IOW, it matters which class is your first class, and there is niche protection--you can't easily overshadow a member of another class just by taking levels in their class--but there's no penalty for being a generalist. There's also defense bonus by class, a new "middle" save progression, and some other minor tweaks. Race is replaced, functionally, by Department, which is the branch of the Agency that you work for. All have a nice flavor, and the advantages/disadvantages are well balanced (moreso than D&d3E races, IMHO).
D20M changes the class structure a bit: it introduces "Basic" and "Advanced" classes. To be perfectly honest, i haven't really figured out how they're different from "base" and "prestige" classes (and i gather that later D20M books have also added prestige classes): the former can be taken at 1st level, the latter have prerequisites. Anyway, the D20M basic classes do one very cool thing: none of their class abilities are fixed. Instead, every other level you can choose one from a list, with some of the abilities rrequiring others as prereqs. And all of those abilities are exclusive to the classes, rather than being available to other classes, or as feats, too. It also makes the interesting decision to have a class nominally centered around each of the ability scores, and gives them sort of lame names. But that's really just a nit-pick. Basically, the basic classes are pretty much just skill packages, and have no flavor--no world-relevance. The advanced classes are pretty much what you'd expect. Except that, since the basic classes "cover the bases", as it were, they aren't meant to be all-inclusive the way those in D&D3E or Spycraft are. This means they tend to be a bit more focused, at the cost of being a bit more narrow. For the most part, i think this is good. Oh, and D20M also has "occupations", which basically replace the role of race for starting characters, determining a couple of minor bonuses/extras. Oh, it also doesn't have multiclassing penalties.
Advantage: Tie. I like the overall implementation of classes and multiclassing in Spycraft better. But it *is* a bit espionage-centric. And there are some very cool class abilities in D20M. I'm thoroughly underwhelmed by occupations, however, and find the basic classes *too* basic. I'd have preferred to see the talent trees that they have access to just written up individually, and each "advanced" class gets access to 2-4 of them, as appropriate for the class concept. But, on the gripping hand, the Departments of Spycraft are, again, very genre-centric. Not a problem for the genre (and closely-related ones: X-Files, action movie), but could be a problem for other modern games. Though they could be dropped entirely (as could occupations) with no real loss to the game, IMHO.
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feats
D20M adds a bunch of martial arts feats, and a whole slew of +2/+2 skill feats. And the martial arts system is, IMHO, so-so. Though the stuff the Game Mechanics have added made me go back and give it a second chance. Overall, i found the feats in D20M uninspiring.
Spycraft has a very cool selection of feats. Skill-boosters are expanded into a whole tree of advanced skillfeats that do cool things with your skills. And there're stealth feats that let you do cool things like full movement rate while climbing. And chase feats that tie into their chase system. And equipment feats that let you get cooler equipment. And style feats that are basically cool social abilities (and blow away all but the coolest class social abilities in D20M). *And* a nice web of feat for the martial-artist that give a good range of flavors while still covering most of the bases, so you don't have to invent new feats for each new martial art.
Advantage: Spycraft.
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Wealth (D20M) vs. Bugdet/Gadget Points (Spycraft)
The wealth system in D20M is very cool. I like it. But then i've always hated counting coins in any game, D&D included. Basically, you have a wealth rating, and if something is less than that, you can buy it. There are adjustments for buying really expensive stuff, and stuff near your limit, and your wealth can go down if you overextend yourself (i.e., you can buy that house that's beyond your wealth rating, but your wealth rating then permanently declines--simulating that you've gone beyond your "spending money" and permanently allocated some portion of future monies to paying for the house).
Spycraft, OTOH, has two systems for costing stuff: Budget/gadget points, and field expenses. Field expenses are just money, plain and simple. Budget and Gadget points, however, are a player resource. Instead of buying stuff for each mission, you are allocated a budget to outfit for the mission--this is stuff you'll have to return at the end of the mission. Gadgets come from a separate pool from general budget, which is for less-fantastical things. The budget/gadget cost and dollar cost don't necessarily scale together: there are things that are expensive to buy on the street, but staples that are easy to acquire from your agency. The beauty of this for the action-espionage genre should be self-evident. But it has a further added bonus: if you don't like an abstract accounting system, it's got prices right there for you. You can just throw out the budget/gadget points for other genres of modern gaming.
Advantage: D20M. I really like the wealth system. However, if you *are* playing action-espionage, or something military, the budget/gadget system is probably preferable for feel. And if you can't stand abstract wealth in your game, Spycraft would suit you better.
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Reputation (D20M) vs. ? (Spycraft)
Here's one place where D20M does better: it *has* a Reputation system. And it's a nice, simple one. However, i wish it did more--as is, it has even less effect on interpersonal interactions than alignment in D&D, IMHO. I wis they'd taken it further.
OTOH, the class abilities and feats in Spycraft mostly make up for there not being an overall reputation system. Despite playing plenty of games with them, i didn't even notice it was "missing" from Spycraft until i started comparing it to D20M, precisely because most of the effects you want out of a reputation system *are* there, in other ways. And often with much more flavor.
Advantage: Spycraft. But D20M has a better framework there if you wanted to build a really robust *and* flavorful reputation/influence type system. But it'd take a fair bit of work [says the person who's in the middle of building one from scratch for a D20 game].
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Ordinaries (D20M) vs. Minions (Spycraft)
Both games have rules for non-PC-calibre characters. But they differ noticably in why they're there, and what they do. Ordinaries in D20M come from the same place as NPC classes in D&D3E: the assumption that PCs are extraordinary, and even the weakest (i.e., 1st-level) PC is better than most NPCs out there. As such, ordinaries are basically weakened PCs, using the same basic class rules, but with fewer nifties: new advanced class levels, random rather than maxxed starting HPs, no Action Points, no class abilities, and a couple of other changes. They're basically ability scores and hit points.
Minions (and "standard NPCs"), on the other hand, are mooks. They are specifically intended to be faceless opponents. As such, they are simplified, rather than weakened, for the most part (though they go down on a critical hit, and can't inflict criticals themselves--but that could be considered as much a result of simplifying bookkeeping as of weakening them). They have the same classes/levels as PCs, and the same stats, but are dealt with in blocks, so all will have exactly the same stats/equipment. Spycraft also has Masterminds, Henchmen, and Foils--see below.
Advantage: Spycraft. But then, i've never liked the concept of NPC classes, or of PCs being inherently better than NPCs, just because they're PCs. More experienced? Sure. But that's what higher level means. A 5th level PC and a 5th level NPC should be roughly equal in ability.
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combat
D20M is basically the same as D&D3E--just as complex, just as poorly explained. And you can still stand up from prone without incurring an AoO, but hitting your opponent's weapon (something you presumably do all the time without intending to during melee) leaves you open.
Spycraft redoes(sp?) the action system almost from the ground up. No more AoOs. Actions are now Full and Half--none of this convoluted "a standard action takes a full round but actually consists of the standard action itself plus a move--which can actually be a move-equivalent action. Oh, and you can change the standard action itself for a move, so you can do a double move as a standard action--which takes a full round. And is different from a full-round action." You get two half actions per round, plus free actions. It clearly explains what is a full action, and what is a half action, and the designations make sense. And the movement rules are incorporated more cleanly. Oh, and the chapter is readable: sensibly organized, with clear explanations and appropriate examples.
Advantage: Spycraft, hand-down.
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gun combat
Both systems introduce rules for such things as strafing, burst fire, and so on. Without going into too much detail here (both are moderately complex), i'll just say that i find those in Spycraft to be easier to actually use, and slightly more sensible. In D20M, you basically need feats to be able to strafe or burst-fire effectively. In Spycraft, those are actions that anyone can take, though there are feats that will lessen any applicable penalties.
Advantage: Spycraft
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Chases (Spycraft) vs. [nothing] (D20M)
Spycraft is almost worth it alone for the chase system. It frickin' rocks! Basically, the predator and prey each have a selection of maneuvers to select from, and you cross-referenc them and use skill checks to determine how they effect the distance between the parties. Also a nice simple system for determining if obstacles come up. And a whole slew of feats and class abilities that tie into chases. It's the first really good system i've seen for playing out movie-style chases in 20+ years of gaming (and, therefore a couple hundred discrete game systems).
D20M has nothing of the sort. Instead, it has detailed tactical-level vehicle movement rules. Great if you have a detailed map of the area, not much help if you want a long chase with high-speed vehicles, however (how many GMs can prepare a detailed map of, say, the Chicago freeways for a chase of the scope of the end of Blues Brothers?). Also not much help for aerial chases. And it abstracts the wrong things (vehicle speed) and not the right things (total distance travelled).
Advantage: Spycraft, hands down. If i was forced to use D20M for a chase, i'd just throw the rules out and wing it with skill checks, because it would be less of a headache.
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RPing and GMing stuff
Spycraft has a whole ton of stuff on running the game. Most notable are the Mastermind system, for constructing a party-appropriate challenge, geared for the length of the "serial" you want to run, and the chapter on "tradecraft" which gives all sorts of great functional and RPing advise on scoping crime scenes, casing places, planting bugs, transportation, etc. Admittedly, much of this is not of as much use if you're not running an action-espionage game, but it still might come in handy. And the "mastermind" system could be used for pretty much any genre for constructing appropriate challenges.
I don't actually have a copy of D20M in front of me, so i'll decline to comment comparatively on GMing/RPing advice.
Advantage: can't say. Spycraft has very good stuff, but it is tailored for the genre. If the equivalent material in D20M is of about the same calibre as D&D3E, i'd call it a toss-up: the better advice of Spycraft offset by the poorer general-applicability. If the material in D20M is significantly better or worse than that in D&D3E, adjust accordingly.
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Overall: Advantage: Spycraft. The only person i'd recommend D20M to over Spycraft is the person who's only really interested in "D&D Modern", or "Forgotten Realms 2000", or whatever you want to call it. For almost anyone else, the only advantages D20M has are including magic/psionics in the core rulebook. And if you are one of the few people out there interested in a modern D20 game, but who doesn't own the D&D3E books...well, maybe i'd recommend D20M, then. Unless you had access to the internet, in which case i'd say get Spycraft and download the D20SRD for magic/psionics. And for the few cool bits in D20M, download the relevant bits of the D20MSRD--mostly the classes chapters--and steal liberally. It's just not worth $40.
Oh, one further exposition of my biases here: i love modern fantasy, especially as represented by Charles de Lint and Harry Potter. I generally don't care for action-espionage--I loved the old Avengers, and go in for detective dramas, but that's as close as i get. So i didn't even bother looking at Spycraft for a year (or two?), dismissing it out of hand. D20M (and Urban Arcana), OTOH, i was initially interested in, because of genre, and probably cut them a bit of slack for this reason.
edited for formatting clarity
Thanks for the compilation
