d20 Modern is good if you want modern D&D style play.
Spycraft is good for any modern/near-future game where the characters are patroned by a huge organization that gives them missions.
I never played Spycraft, and I don´t have the rulebook, but I played D20 Modern. Our Master decided to use a Dark Conspiracy adventure, the Heart of Darkness. I don`t know if anyone of you knows it (our master bought if several years ago, but never mastered it because he wasn`t fond with the Dark Conspiracy Ruleset), but the players are part of a organization that gives them missions - the organization is not as huge as the CIA or KGB, so you can`t expect the "cool stuff" like James Bond Aston Martin.
It worked perfectly with D20 Modern, as far as I can tell.
In regard to Wound / Vitality Point -
I do not like it, and I am not unhappy that D20 Modern does not have it. (au contraire, monsieur)
It did not fit in any of the typical movies and series we know - especially the rule on critical in Starwars seemed to be a very stupid idea - (how often do we see a hero being killed by a blaster shot? Never, I think, is the right word for it.
And do not tell me that Leia had a fair chance of surviving a critical hit with a Blaster Rifle when she was shot on Endor ...)
The D20 Modern Rule seemed fine with me - the characters have, at any level, a certain risk of being shot down, so it weakens the typical D&D syndrom of having so many hit points that nobody has to fear weaker opponents...
But for the nonlethal damage rule - that does not work, thats true. But I do not know many games where we hadn`t to implement a house rule or two...
Mustrum Ridcully