Starcraft is pretty good. CnC3/Kane's Wraith is a staple for me.
Dark Reign used to be one of my favourites, but in retrospect it kind of tried to do too much at once.
Netstorm was one of the most brilliant RTSes I've ever played, but it's just plain too weird for most people.
TA has a weird combination of designs and features that were 10 years ahead of its time and a few bits that weren't.
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