I am a huge fan of Spycraft, and have not actually read d20 Modern (as my wife calls it blasphemy, she's a bigger Spycraft fan than I am). But, I've read my share of this argument, and here's how I see it breaking down.
Spycraft is cinematic. Period. It supports cinematic extremely well (action dice being key), but it needs to be tweaked to allow for realistic, gritty action. d20 Modern is more flexible, but consequently doesn't support any particular style as well. It's a breadth vs. depth question.
Spycraft's design philosophy focuses on offering up each new rules set as a self-contained nugget, that you can use or ignore at will. This makes it very much a toolbox. You can mix and match tools to not only fit your campaign, but your individual players (running infiltration as a straight skill check, use the streamlined infiltration rules, or actually play it out, depending on the interest in and the importance of the detail). Add up a certain set of tools, and you come up with a particular campaign flavor. d20 Modern, on the other hand, attempts to create a very integrated, but very generic, system. So, you use the same tools for every campaign (tweaking for levels of tech, magic, etc. of course). Much better rules consistency from campaign to campaign, but less change in flavor.
Spycraft assumes that the characters are highly trained operatives at 1st level. It also is scaled as much as possible to allow the characters to continue to get scarier as they increase in level (e.g., many more high-level feats than D&D offers). 16th-20th level characters really are super-human. d20 Modern assumes that characters are average Joes when they start out (hence, the base classes of Fast, Smart, Strong, etc.). Consequently, they also cap out sooner. You would really need to re-scale the system to properly portray James Bond or Batman. OTOH, it would be nigh-impossible to create Xander Harris or most any horror-movie victim/hero as a PC in Spycraft.
Mechanically, they both have good points. Spycraft has a VERY clean combat system. I also really like what they did with feats (breaking them down into a number of categories, and including a lot of Skill, Gear, and Style feats for people who aren't all about combat). OTOH, from what I understand, d20 Modern's wealth mechanic is much cleaner than Spycraft's BP/GP system.
Spycraft: If you want espionage, there's no question. Otherwise, it's good for highly cinematic games, especially with significant military or pseudo-military action. Personally, I think the mechanics are better in general.
d20 Modern: If you want a game of average Joes caught up in events beyond their understanding, this is the better game. Also, if you want a very gritty, realistic game, this might be the better choice (personally, I hate grit, so I generally don't look at those aspects). Finally, if you want a lot of magical elements (Buffy, Vampire: the Facade, Shadowrun), this has the advantage of already having the mechanics built in. I don't think they are superior quality, but at least the work is already done.
Oh, and on the point of 3rd party support, Spycraft will be getting significant 3rd party support soon. Paradigm is releasing two sourcebooks this year (Most Wanted and Combat Missions). A few other publishers are looking at the "Powered by Spycraft" option AEG is putting on the table. Expect official announcements later this year. (This is the word from the Spycraft GM seminar at Origins.)
