Command and Conquer 3 for sure.
Supreme Commander is extremely overrated, I found it quite horrible to be perfectly honest.
Command and Conquer 3 is a nice game though, I'm currently plowing through the Nod campaign (the campaigns are very well made).
But since I'm not an RTS genius I usually go for the newbie tactics (building mass defense until my base is invunerable, then attack!

) so it's taking me a while.
The cutscenes are great too, adds flavor to the game.
It's not as good as Red Alert 2, but it's pretty close I think.
If you're getting one of these games I recommend C&C3, which is an overall better game.
EDIT:
stevodotorg said:
I have played the demo of C&C3.. and for some reason, I just didn't get into it as much...
I played the demo for C&C3 too an wasn't impressed, but then I tried the full game in the Nod campaign, it totally changed my mind about the game.