Starcraft 2 is the best of the bunch, if you want to get competitive, or if you want the best RTS campaign in recent years, the story is cheesy but thats how it goes with Blizzard, or you can play at the arcade with the vast amounts of mods and custom maps.
C&C 3 with the expansion is also a good one. Also, Supreme Commander Forged Alliance and Total Innihilation.
While not a spehz-RTS, if you do pick C&C3 up, be sure to check this out:
http://www.moddb.com...iberium-essence
Runs with the base-game, and renders the official expac somewhat obsolete, to be had. Besides, Tiberian Sun-era units in 3D. 
Original Star Wolves was a nice, little game I played back in the day. Far smaller in scope than the mentioned Homeworld, but it wasn't bad for what it was (there are sequels, which were rather meh though).