Homeworld, unequivocally. Granted, the second game wasn't quite up to snuff, but the first game is still the best RTS out there. Utterly perfect blend of gameplay, art, story, music, multiplayer, and every other aspect that makes an RTS an RTS.
I'd have to say the MechCommander and Company of Heroes series are pretty damn high up on the quality meter as well. Sins of a Solar Empire is also absolutely fantastic, but it's one game, so it can't quite be called a "series". However, a sequel could change that.
