Others have commented on systems, so I won't go into great detail.
HERO is my system of choice. It has more supplements (and in general better, but with a caveat later). If you haven't played the system for years instead of going for the huge base rulebook use Sidekick. It is a trimmed down (slightly) version of the rules, and it is written to help someone new to HERO learn the rules, whereas the 5thed Revised is written for someone who knows the rules, and as a reference manual. Sidekick is also only 10 bucks. Can't beat that.
Other really nice books in the line - Until Superpowers database which is basically writeups of a bunch of powers in HERO terms, useful for the beginner.
Champions is a sourcebook with all sorts of advice on running a superhero game, and discussion of archtypes and such - it does not contain the rules of the system though - those are in 5er or Sidekick.
There are 3 city/area sourcebooks, a campaign book, a number of character/orginization books, and a number or subgenre books (teen champions and galactic champions).
M&M would be my second choice - although I dislike the damage save. It's character creation is very flexible, and fairly intuitive (although that is coming from a longtime HERO player, most point buy system are fairly intuitive to me). All of the support material out right now is for 1st ed.
The caveat I mentioned earlier- I personally don't like the feel of the Champions universe. It comes off a little to Iron Age for me - not the big gun toting stuff (thankfully) but it is a litte darker than other campaigns I've seen. Freedom City is one of the best campaign settings out there - I use it as much or more than I use the Champions Universe in my champions games.
And the absolute best superhero/character supplements being written right now are out for both systems - Blackwyrm Games' Algernon files supplements. They have a different version of thier books for Champions and for M&M - so you can get the great stuff for whichever of the big two you decide to play.