You've asked the right guy, good buddy, RTS is definitely my genre of choice. 8)
Star Wars: Galactic Battlegrounds - My current favorite. Although I am a Star Wars fanatic, this game is sweet no matter who plays it. My friend's dad plays it religiously, and he isn't that big a Star Wars fan.
Command and Conquer: Generals - This game is also friggin sweet. Modern day RTSs are sweet...sweet to the max. ^^ I also heard the expansion to this was damn good.
Age of Empires II - A classic, and I swear by it. I wouldn't play without the expansion, but after you add that in, hours of fun in the making. Online play is sweet as well.
Warcraft III - This one is ok, although I'll only play it online. Otherwise, it's too damn frustrating.
Stronghold - This one goes skipped in many RTS discussions. So detailed and masterfully created, it's my definite second favorite. Also, a sequel is coming out, so keep your eyes peeled. :wink: