Well, my all time, absolute favorite system for Super Hero games is Mutants and Masterminds, 2nd edition.
The CharGen is point based, but nowhere near as painfully obtuse in spots as HERO (which is also awesome), the powers, feats, and bonuses are flexible enough to allow you to make nearly any kind of character (I've played everything from an alien space police catgirl who could punch out Luke Cage, to Solid Snake, to a very thinly veiled X-23 to a D&D-style barbarian), the system is pretty simple for a d20, and it handles things very well, in nearly all respects.
What it is *not* good for, however, are things in the horror genre, or when you attempt grit. It's perfect for the average super hero game though. One thing, though, is that if your players are new, you'll often see a lot of the same numbers, as power rank and attack bonus (barring trade offs) are capped at your power level for the game, so it can be somewhat boring to look at, number-wise.
HERO is a much more in depth system than M&M, and equally harder, I find, to run and make characters in, but it allows more precision and customization, as well as having some utterly amazing supplements.
