My vote's for Four Color to Fantasy.
The key point is that you can use it with other d20 games, to help finetune the kind of superhero game you are trying to play. When used with d20 Modern, it takes advantage of Modern's flexible class system, which gives you a lot of options for creating the exact character you have in mind. (Especially since characters with more 'normal' levels are likely to have more skills and feats, which better represents more actual training and skill.)
For normal, modern superheroes, either for four-color or for a darker, edgier kind of superhero game, I'd reccomend Four Color to Fantasy used with the d20 Modern rules.
With D&D, it's very easy to use Four Color to Fantasy to simulate Wuxia or similar high fantasy, and with its rules for Mystical superpowers, helps smooth the edges of D&D's Vancian (or semi-Vancian) magic system, by allowing simple things like a Wizard or Sorceror being able to fling an unlimited number of small bolts of energy, or other similar small magical feats that shouldn't take up spell slots.
I have very limited experience with Spycraft and most other d20 games, since most of what I play is D&D or some variation of d20 Modern. However, given the flexibility and portability of Four Color to Fantasy's rules, I'd suspect it would work well in most any system.