Deeds Not Words is a 300+ page pdf for $10 that does an excellent job in staying in traditional d20 rules (classes, etc..), while fitting extremely well with the supers genre. I never thought d20 and classes could pull off a supers games (I'm a die hard Gurps/Champions or Fuzion Supers fan) but DND did it! The site is:
http://www.allforart.com/cryptosnarkgames/main.html
Scott Lynch (of Cryptosnark Games) is releasing a 1.1 version early next week, which is free for all previous purchasers.
I have read all of the other d20 supers games out there, and if youwant something that really fits the d20 system AND the genre, than DNW is my choice, bar none.
MnM is great, don't get me wrong, but If I wanted to play a supers game that is not easily compatible with all existing d20 material (without conversions), than I would play another system all together.
FCtF is also a good choice, but I don't think it lives up to the SUPER in Super-hero. It is great to add minor powers to characters if you are playing a grim and gritty d20 Modern supers game (which I may do), but it does not hold up to playing characters of say, X-Men (or even New Mutants) ability levels.
But I'm beginning to ramble, so...