If you're looking for something to use in addition to the rules you already know, I suggest E.N. Publishing's own product, Four-Color to Fantasy, which is compatible both with core D&D and D20 Modern. The modern edition just went on sale at RPGNow.com, and it meshes easily with the existing rules systems, making it very flexible.
You can use it to run a superhero game, or you can use it to balance any sort of special power you give to your PCs that doesn't fit with classes (for instance, in my home game, some of the PCs have permanent magical flight because they were subjected to an aeromancer's experiments), or you can use the rules to design monsters. The key point to FCTF is that it's a toolkit; the rules are written primarily to be used for super-powered games, but they're equally well-adapted to putting them in normal fantasy games as special magic powers, or modern spy thrillers as nifty gadgets or genetic mutations.
If you want a game that's designed just to handle super heroes, specifically intended to capture the comic book pulp superhero feel, you might want to look at Mutants and Masterminds. It won an ENnie for, like, everything, and it's really a great book. But the rules are designed to be used on their own, so it requires a little finagling if you want to use them in a game outside traditional superheroes.
In my experience, and this is not intended as a slight to the authors, both Vigilance and Deeds Not Words are too clunky and specific, designed for certain types of games, and not quite a proper fit for other types. As for Silver Age Sentinels, I haven't read it, but I really don't like the cover. It's like you've got a bunch of guys standing in the way between you and the book. A bad design choice.
MnM has the best cover (highest budget), followed by FCTF (done by my ex-girlfriend and aspiring comic artist).
