Company of Heroes (+ Opposing Fronts) — 2007
Better than Dawn of War by the same THQ-Relic get-together. Troops seek cover and all that. It's like someone slapped the spoon of realism around in what would be a typical RTS and actually got it right for once. My only complaint is the Sherman tank, which seems blatantly overpowered (Americans made the game, hint hint), especially when you stick then long 76mm gun on it...
Medieval II Total War (+ Kingdoms) — 2006
Tun-based campaign map, but it still fits the RTS category since actual fighting is real-time. Better than its predecessors, in that provided you've got the game running smoothly the soldiers will actually fight each other instead of go through an animation where they swing their weapons around. A lot of units, a lot of nations, the whole of Europe (and parts of the Americas) to fight on... and one word: Crusades.
Homeworld 2 (+ user-created mods) — 2003
What Relic did while they were with Sierra, or whatever, was make the greatest space RTS ever... seriously, there are not enough of these (and actually, the first Homeworld was apparently better). If you've played the game it speaks for itself, but if you haven't, you've got a 3-D battlefield where vertical attacks can easily be implemented. As far as the playable races go, the Vaygr are horrifically underpowered in multiplayer, but then, multiplayer was never the highlight of the game in my opinion — the vast modding community is where it's at; there's even a Star Wars mod.
Command & Conquer: Tiberiun Sun (I never got the Firestorm expansion... lol) — 1999
It's a C&C game, 'nuff said, yes? Red Alert's skirmish mode was terrible in my opinion, Tiberiun Sun seems to have fixed a lot of those things.
Uprising: Join or Die — 1997
It started here for me... it's an RTS-FPS hybrid, but done in the way that it works well enough as both (the ability to directly control allied units being the only thing missing). Great graphics for its time.
I'm gonna have to explain how this one works... Basically you're in a tank (Wraith Assault/Command Tank) and you go around capturing these 'command bunkers' where you call in a turret called a Citadel and order the factories to be dropped in the available slots (ranging from one to three). Apart from that, all you do is spam your units at the enemy bases (all units except Bombers teleport in), protect your own bases, and of course pick off your own targets of oppertunity using the weapons you took with you (if you bring enough you could erase a whole enemy base yourself, but usually as a consequence your allied units will be less powerful since you've only got a set amount of points for a battle in quickstart).
Okay that's my rant over... Wow, I typed a lot of crap. :D
Oh yus, my favourite one is Uprising.