One note here - I realize I have neglected to mention GURPS Supers. GURPS is a fine system - I like it and have played multiple campaigns in it, mostly fantasy. I think it excels at low-powered games and falls apart with higher-powered ones. I have most of the 4th edition books and I am told it handles high power much better than 3rd, but I have yet to try it. I just never liked the flavor of GURPS Supers. tried it, didn't like it. Plus it wasn't really a game line on its own, just one book in a larger line with minimal support.
The 2000's saw a rather surprising (to me anyway) wave of new superhero RPG's. By the end of the 90's TSR went under and so the Marvel Game went away. DC went dormant. V&V disappeared years before. Champions was still rolling along and rolled out 5th edition in 2002, and Heroes Unlimited was still in print, but that was about it by the end of the 90's. West End did a DC Universe RPG using a different system but the game came and went in 3 years so I don't know a lot about it and never played or ran it. Pinnalce came out with Brave New World which had a great concept but the system was similar to Deadlands and just didn't feel very Super in my opinion. It didn't last long either.
Then in 2002 we got TWO totally new super RPG's - Mutants and Masterminds based on d20 mechanics but using a point-build system like Champions, and Silver Age Sentinels using Tri-Stat mechanics and a build system too. That was also the year 5th edition Champions came out so it was a great year for super-systems. Godlike also came out at the same time.
I picked up M&M 1st edition and liked it. I ran some sample combats but we were heavily into D&D so there was no way to make it a regular game. I loved the presentation though and though it was the best looking supers game since Marvel. Until I saw SAS...
SAS was to me the high point of supers game presentation. I love the history of comics, I love the chapter headers presented as old comic book covers, I like the artwork in the book, the character presentations, the page edges colored by chapter - it's just better done than anyone else. I like the system too, but it was hampered by a lack of support. I would still happily play or run it today though.
M&M got some very nice support then it went to a 2nd edition in 2005 and got a lot better. It did touch one of my pet peeves though - I really dislike game systems jumping to a new edition after only 2 or 3 years, games like Shadowrun 1st to 2nd, D&D 3 to 3.5, etc). My dislikes aside the game was a little wonky in places and 2nd edition was a big improvement. M&M is still going strong and I would guess that it's the #1 Supers game today as far as sales.
Godlike came out about this same time and is another great game although more limited in scope, focusing on supers in World War II. Being a history buff and having a particular interest in WW2 this is an awesome game to me and uses the One Roll Engine system which I also think is great though I suspect it's a little strange in play. Power levels are lower and there isn't a ton of support but the concept is awesome and the background is great.
The problem with these newer games is that I haven't gotten to play many of them. I have books for all of them, I like them, but I haven't been able to string together players and time to run a campaign using them. Hopefully NE will open things up like this after we complete it.
The most recent supers game that caught my attention (besides the above) was Necessary Evil for Savage Worlds. It came out in 2004 and was rereleased in 2009 in a slightly updated form. I really like the Savage Worlds system after trying out some fantasy combat with it and after seeing the campaign concept I was sold. it's taken me 6 years to get there and it's been over 10 years since my last supers campaign of any kind, but we're finally there and I am very happy about it.