Hmm.... I have played neither, and I just got d20 Modern with my Xmas money. So I am not too up to snuff on it, but here are my impressions.
d20 Modern is a Tool Kit, Spycraft is an Espionage game.
Classes:
d20 has very generic concept classes. You can make any character concept with a mix of basic and advance classes. However it may take 3 to 5 levels to establish your character concept.
Spycraft, you character is one of the pre-established archatypes. Now these archatypes are very felxible since there is a lot a feats, but you still have to pick one of their general Archatypes.
Skills & Feats:
For the most part, they are the same. Some slight variations. (ie d20M uses Craft(Mechanical) where as Spycraft has Mechanics.) the Surveillence skill is unique to Spycraft, but it is a genre specific skill.
There are more feats in Spycraft, but those extra feats are for the genre or have to deal with the different combat system.
Combat:
Both are an improvement and clarifaction over DnD 3e combat. Spycraft simplfies things to Full, Half and Free actions. d20M uses Attack, Move, Full and Free actions. Effectively Spycraft combines d20M's Attack and Move Actions in to a simple Half action.
d20M grants iterative attacks based on the BAB of the character, Spycraft gants additional attacks tough the selection of Feats.
For the most part, I like Spycraft more then d20 Modern. But d20M is still a very good game. I would happily play either. Both are solid systems, so it is mearly a matter of taste which way you want to go.
=--The Luddite