Company of Heroes is a lot of fun. My all time favorite, has to be the Age of Empires series. Had a lot of good games in there. Another, different kind of RTS is World in Conflict.
I was a huge fan of Age of Empires for years, but I think that train sort of got off the rails with the later versions. I loved the old Roman armies, the Greeks, those ships, and all that stuff. I wish they'd update that version of it instead of making such big changes in the format. I didn't care for the whole North America thing at all.
Oh wow. I completely forgot about World in Conflict. It's not your typical RTS since you only control units and command one aspect of the Army (Infantry, Armor, Air, or Support), but it's a very team-based game and fun to play. The story is also fairly well written and I really like the way the campaign plays out, especially if you have the Soviet Assault expansion.