I've played most of the major ones over the years, though some far more than others. I've never really clicked with the heavier systems like Champions. They just don't feel like comics to me.
My favorites that I've played recently:
- Galaxies in Peril- this is a Forged in the Dark take on superheroes, and it works surprisingly well. The system for powers is almost absent... you simply pick what kind of powers you want, that fit with your playbook, and that's it. It works really well. I think the default setting could be tweaked a bit to better suit the team and downtime elements, but other than that, it's a highly functional game and we had a great year-long weekly campaign of it.
- Marvel Superheroes RPG- the classic by TSR. I broke it out recently to play with my 6 year old. The game not only holds up really well... I think it was ahead of its time in a lot of ways. Degrees of success, player facing mechanics, player resources to influence play. The whole karma system to incentivize decision making and present difficult choices. It works really well, it's very simple, and also robust. Absolutely a blast to play and it flows really well. For the most part, all you need is the Universal Table to run a game.
- Masks- I only played two sessions of this, but it's a fantastic game. As others have said, it's very much focused on the identities of the characters more than just super-heroics. But that's what makes it so compelling. Most superhero comics... or most good ones, anyway... aren't just about the powers and the fights. They're about the characters. And this game ensures that happens... play is absolutely about the characters and their identities... not just the superhero masks that they wear, but the kind we all wear.