orcishgamer: Sacrifce or Giants: Citizen Kabuto. Both really.
+1
I always recommend these two any chance I get. Be advised though, that neither game is a classic RTS.
Giants: Citizen Kabuto is... hard to define. At its most basic level it's a first/third person shooter, but as the game progresses other gameplay elements are introduced, among them squad based combat and base building. The game has a story like no other, and a sense of humor that's absolutely hilarious.
Sacrifice is a... third person RTS, I suppose. Combat is done using spells and summoning creatures to fight for you, mostly the latter. The game has a fantastic story and an interesting setting, with a unique visual style. Plus, it has a high level of replayability, because your choice of missions affects both the story and which creatures and spells you have at your disposal.
Both games are terribly overlooked gems in gaming history. They are rare examples of developers saying "Let's do something radically different, for a change", and the results are amazing.