Well, I'd say the SRD gives you a good idea if you know what you're looking for in game mechanics, but I'm not getting into the middle of this one ...
Just ran a pulp 40's Spycraft game last night. I've run a couple Dark*Matter d20 cobbled-together games,all based on pretty much what I'd gleaned from messageboards and Polyhedron articles, but turned out to be almost dead on. So I think I can compare.
This is not advocating one over the other -- the question was about integrating the systems. I concur with Digital Dark, and offer a little advice sampling the two based on my experience.
First off, the rules match the tone. Captain America and James Bond are Spycraft, not really d20Modern (one might argue they're DNW...

) The choice is, IMHO, what game you're going for -- "Yikes, people are shooting at us!" is d20Modern, while "YEAH! PEOPLE ARE SHOOTING AT US!" is a tad more Spycraft.
They can be blended.
-- Add the Spycraft feats like a spice for deadlier combat and more hyper action. Unarmed combat's damn tough in D20Modern, so I'd sample to flavor if you want gun-fu.
-- The Spycraft classes are okay, but the Snoop/Fixer crossover's always been a little weird for me. These classes or for a SPY GAME, and not really anything else. You'll note the Spycraft expansion books are introducing new base classes every book to cover different options.
D20Modern's a LOT more flexible yet less heroic. Probably, your D20Modern characters need to be three or four levels higher than your Spycraft characters in order to handle the same threat.
--use the d20M Skills for the blend or, frankly, for either game alone. (sorry, Spycraft, but there are just too many skills, it'll spread the Skill Points too thin) Really, you can't compliment the D20M guys enough here; this skill list, with the tweaks for tech, will replace my D&D skill list. For using versions of the skills requiring the Wealth system in a non-Wealth system, look to the Star Wars game for an adaptation
-- Personal combat: Tough to argue with the Spycraft streamlining, and the sytem's BUILT for firearms, not ADAPTED to firearms. All those gun options "Cover Me", "Keep his head down", etc, are organic and well handled.
Personally, I'd use the Autofire rules from d20Modern (never liked the -2 a square in Spycraft), but consider changing the BURST feat Prereq to a BAB or Weapon Focus rather than a WIS +13. Most people aren't noticing that the feat allows you to point a gun with a brutal recoil at an opponent and HOLD IT ON HIM, as opposed to just hosing down an area, so I don't have as big a problem with that requiring a feat.
I like the Armor DR rules in Spycraft -- particularly considering the "nonlethal damage" and "massive damage threshold" rules. Losing Subdual as a Game Mechanic is a pain in the butt, but it's your game, slap it back in at will. Once again, I don't think it's a big mechanics thing, more game flavor. The joy I as a GM have describing the brutal impact of machine-gun fire slamming into a character from behind is important to the gaming experience.
Just remember -- two attacks a round at your base attack is much deadlier. MUCH. Two bursts from a submachinegun is potentially 8d6 of damage, and a first level guy can do that.
-- Vehicle combat ... arrr. For a chase, Spycraft wins hands down; who the devil wants to sketch out exactly the intersections and off ramps on a battle map for the character-style vehicle rules of D20Modern? On the other hand, for tactical, multi-vehicle free-for alls, the nod must go to d20Modern. Someday I'll get that system blend done, throwing in the excellent Dragonstar rules (and ayone wanting to run a futristic campaign should look at the two new equipment books for Star Wars and Dragonstar, both great ...).
I would at the least suggest stealing the "Open, tight,closed" terrain/obstacle rules from Spycraft. Weirdly, a variation of this system was in the Pulp Adventures in Polyhedron, but was not used in the game.
I also like the Spycraft penalty to a driver who mucks about doing stuff and not just focusing on driving. Again, what you choose form here is what's appropriate to your campaign.
-- Wealth system is a great world system, Budget points in Spycraft good for a group who has the resources of an Agency. Again, there's probably a conversion/combination lurking in the wings somewhere.
-- I like the Spycraft Psionics system, but I'm biased toward Feat-and-Skill based Psionics. Introducing more classicly "psychic" abilities to the Psionics Spell List (and it is a spell list) in D20M to flavor probably isn't a bad idea. But if you're going to blend the two, choose one or the other. Your third level Spycraft Telepath will flash-fry your third level D20Modern Telepath, waving his little Bear Claw around. "Grrr...."
-- Magic's too campaign-based to be factored into a comparison of the systems. Thirst and Fringescript are cool, but definitley meant for NPC's with the rules for PC's done somewhat grudgingly.
Have fun.
John