AoE and AoE II were good. I also played SW: Battlegrounds and liked it...however, after that RTS just fell out of line with me. I bought WC III and Starcraft recently. Starcraft= awesome, but (to me) WCIII= okay. However, my computer hasn't been upgraded for years and (sadly) I fell out of the computer and RTS loop.
I played a 'Goblin Commander' game for the PS2, though, which I have to admit I really liked.
EDIT: I forgot to mention Age of Mythology. That sucked me in for a while. Empire Earth was really great, as well, and so was an older C&C game I played.
So I guess what I'm saying is, most RTS I play I love but suck at for some odd reason.