Blindrooster said:
The old Star Wars: Galactic Battlegrounds. Hands Down.
Easily the greatest AoE2 mod that I ever spent money on.
But yeah...
Since you already talked about Age of Empires, Supreme Commander and Starcraft, I'll go with things not yet listed as of 11:30pm EST.
If you decide to play anything in this thread, let it be Sins of a Solar Empire. It's the greatest mix of 4X and RTS gameplay I've ever seen, even better than Sword of the Stars (another great one). If you like Master of Orion, give it a shot.
Command and Conquer series is really good, especially Red Alert. Classic and still fantastic.
Company of Heroes is also a great series. Probably the only RTS that made me feel for my troops.
The Earth 2150 games were very interesting, they had sort of a dual-layer map with underground tunnels and stuff.
Original War is more of a RTT but there's base-building in that.
Warcraft III, Homeworld, and Dark Reign II come to mind as fantastic "standard" RTS games...
D&D: Dragonshard is pretty cool too, Battle for Middle Earth is very good (Especially BFME2).
There's a lot I'm not mentioning, but suffice to say I love RTS games and I still think TA was lightyears ahead of most games in the UI department, and Supreme Commander's "Tactical Zoom" really makes it hard to play any RTS without it. I liked how R.U.S.E. did it too.
Anyway, I cannot name a best. It's impossible to name a "Best" when there's so many base-building RTS games out, and they're ALL SO DAMN GOOD.