Starcraft is a unique case IMO.
Arguably the only reason its gameplay ever got so deep, and the reason it's still being played today as much as it is, was because South Korea went batshit crazy over it - something nobody could've predicted, least of all Blizzard. Largely (if not solely) because of this, it's been patched for 12 years, and obviously is one of the most balanced RTS games ever made - hell, a game better be balanced if it's been worked on for over a decade. Kinda makes you wonder what one could've uncover in games like Total Annihilation, Dark Reign or the C&C games, had they had a country start worshipping them.
As for the topic:
Since I've played quite a bit of RTS games, it's hard for me to pick just one best RTS. So here's a bunch of 'em.
Single Player:
C&C Tiberian Dawn
C&C3: Tiberium Wars
Red Alert 2: Yuri's Revenge
Total Annihilation
X-Com: Apocalypse
Warcraft 3
Warhammer 40K: Dawn of War
Multiplayer:
Warcraft 3: DotA
Total Annihilation
Supreme Commander (even though I'm not that good at it)
DoW
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