I was pointed at SpringRTS about a week ago by a friend of mine (who's actually a windows user, which I guess already says something about the quality of the game). I'm surprised it's getting so few attention around here, especially since everybodys always complaining about the lack of good non-fps games like rts for linux. With SpringRTS there are even several at once available! Though I've got to admit I've only played the Balanced Annihilation mod so far, but that one is really nice.

Other favorite games of mine:
Nexuiz (hands down best quake/ut clone imho)
Penny Arcade: On the Rain-Slick Precipice of Darkness
World of Goo