In my opinion, Company of Heroes is probably the most in depth and detailed RTS I've played.
But my favorite RTS is Age of Empires III: The Asian Dynasties. One, because its got a lot of unique ideas for the genre as a kind of mix of Age of Empires II and Age of Mythology with a 'deck' system added. Two, Because it seemed to fix every problem from Age of Empires II (refreshing farms, unit AI, more unique ships, hero units for exploration, etc). And three, because I'm actually good at the game.
I feel its really sad that AOEIII never took off. And I attribute that mostly to the 'sequel effect' and people not wanting to get off AOEII. Same thing as Smash Bros Brawl, FFVIII, Chrono Cross, etc. However, having said that, I know there are other reasons the game didn't take off. ES Online is REALLY laggy and MS put some rediculous piracy protection on the game so even two people with the same build of the game fresh after install will get a 'RCR Mismatch' error and can't play the game, on LAN of all things. Also, the game was released in parts and didn't become the awesome game it is now until the Asian Dynasties expansion.











