I loved C & C Generals. China vs. the US vs. the GLA (a stereotypical terrorist group). Fight with F-22s, Apaches, Tomahawks, MiGs, chainguns, napalm, anthrax, bwahahahahaha…
Futuristic RTS, proper 3D graphics, great missions, units and a huge fan base for a game of its age (meaning lots more units and maps for the game) Very playable and a lot more control offered over events than something like C&C.
Also, although I have not had the chance to play it, I have heard good things about the game Trash. It’s considered an independent game, but it’s also been described as the intellectual heir to Starcraft. I think there’s a free trial at inhumangames.com.
Not only is Total Annihilation good for the theme in that it’s modern/futuristic, there is no better RTS. Thankfully, I haven’t needed to play an RTS (except Space Rangers 2, special case) since.