The FATE system, as a modification of Fudge. I believe it was first published in a product as Spirit of the Century's system, but before that I coded it for use in a Star Trek online game (PennMush, if anyone's interested). It was an absolute blast. I got to play an El Aurian, so, there's that.
The ability to focus on the story and use
that for narrative control is maybe not as revolutionary as it once was, but is still a powerful tool for player involvement and steering dramatic scenes in directions satisfying to all involved.
When it comes to mechanics and the statistics thereof, I still find L5R's roll and keep system fascinating. I haven't been able to pin down why I love the mechanics of that game, despite many hours of dissecting it. I have not had a chance to examine 4th edition, only 3rd.
Exalted 2nd ed. I love that game. Seriously. It's mostly the setting because the mechanics are frustrating -- a tactical RPG where the authors of books beyond the core did not have as strong a grasp on tactical design as the original. The setting is what drew me in -- that and heaps of dice. I can go into more detail, but if you're not familiar with Exalted it'd be just me rambling. Even with all that, it does tactical superpowered fantasy combat very well. Quite a lot of work on the GM's part to create challenging enemies that don't steamroll the party or get ganked in 5 ticks by a team of well-coordinated Exalts. It's still the Storyteller system, though the numbers are tweaked a bit.
And finally: Star Wars Saga Edition. What D&D 4th ed should
have been. As mathey mentions, Talent tree system snagged from d20 Modern truly comes into its own here. Chargen is actually fun, doesn't take long, and there are infinite options. Multiclassing is recommended, and it's almost impossible to make a bad character. The mechanics are well done, even though the authors would like to go back and change a few elements knowing what they know now. The Force point and Destiny point systems are central to making the heroes feel like they're roleplaying in the Star Wars universe -- but FATE can do that just as easily.