Overall? Lets be honest here, almost certainly World of Warcraft. The games probably got around a hundred songs now and you just can't match the kinda budget Blizzard are able to throw into these things. Full orchestral scores directed by professional composers and with a budget that probably topples many full motion pictures! I don't even play WOW anymore and haven't in months, but I'll admit to owning the soundtracks and listening to em every once and awhile regardless.
Still, wasn't actually all that impressed with the Starcraft 2 soundtrack. Go figure.
ANYWAY, Blizzard aside, I've always been really impressed with Relics work with the Dawn of War series. It's just so damned ambient and perfectly fits each race its meant to represent, whether brooding and heavy like the Chaos theme:
Or the more dramatic, mystical soundtrack of Eldar in Dawn of War 2:
Actually... now that I think about it, RTS games in general tend to have amazing soundtrack. Hell, even WOW's soundtrack is built from the music made for the previous Warcraft rts. And then there's Age of Empires, which had some of the most moody and beautiful ambient pieces I've ever heard. Don't believe me? Just listen.
So mellow and relaxing, mmmm...