Any Relic RTS for mixing up the formula just enough that it's fresh but still instantly familiar. CoH nailed atmosphere like very little games manage to, especially RTS games. You didn't feel you were playing an RTS so much as you were fighting a bloody war with real people dying. Very very awesome.
And then there's DoW2:Chaos Rising. To date, the only RTS (and game actually) that had a proper morality system in place. It wasn't arbitrary (well as much as the imperial laws are), it had impact on both gameplay and story and was awesomely done. Most games have the idea of morality wrong, they present good/bad or whatever they call it as two same choices, and you pick whichever you feel like, they maybe impact the story or some of your abilities, but you rarely get a really really tough choice that tempts you to go the other way. CR had this, since going corrupt had tons of boons for your squad, they'd get new abilities, more powerful gear, and in certain cases missions would be easier if you did the bad thing. As such, the struggle to remain pure was accurately depicted, suddenly you realise just how hard it is for the Marines to remain loyal, when giving in to Chaos is so easy.
Another great touch is how the ending itself is affected, you don't immediately realise how corruption is affecting the story (apart from the prevalent everybody could be a traitor stuff, but that's always present in 40k) until the traitor is revealed. And then you realise that your strongest unit/champion the one you kitted out with all the cool stuff has turned on you, and now you have to fight the monster that you created. Even when you do defeat him you still have to win the rest of the mission (which is kinda annoying towards the end) and then you realise that your troops still aren't safe because they're all now under suspicion for treason, because of your actions.