I have so many answers!
There's the Homeworld series, which was beautiful in every way, from sound to visuals to mechanics, just such a perfect 3D space based RTS. The destruction of Kharak is one of those real defining moments. Cataclysms beast tried to actually give the RTS genre a horror twist, and I feel it worked, especially given just how much effort the voice actors put into it - and homeworld 2 concluded the story with a distinctive art style and more top notch design.
There's the Age of Empires games which I've sunk so many hours into, which taught me the basics of RTS gameplay, and which pretty much framed every experience I've had with the genre. It gets it right on so many levels, that unit and counter unit struggle and manages some really epic battles for its time.
There's Rise of Nations which took AoEs idea and shaped it into one of the best RTS games I've ever played, taking it from a classical/medieval RTS to a global, risklike game of world domination, with loads of factions that all played differently and enjoyably, and had an interesting, if rudimentary supply system that made forays into enemy territory a risky venture. It's also one of the first RTS games to toy with infinite resources and a struggle for territory - not the territory control of Dawn of War - mountains, forests and oil deposits would be fought over, to expand borders and grab the tasty land. The idea of never destroying an enemy town, but capturing it, to grab hold of their production capability... great ideas in a great game.
There's Dawn Of War, which is a blisteringly fast RTS and introduced the reinforcing unit concept - where units weren't simply disposable but precious investments, the loss of a single one could be a critical turning point in any game. Diverse, diverse factions meant some poor balance, but the core of the game was brilliant, and battles never lasted so long as to become tedious - the back and forthing always engaged.
Company of Heroes refined its concept further, adding a veneer of pseudo-realism to the proceedings, as the axis squared off against the allies in pretty, soon to be ruined french towns - viscerality was the name of this game (other than Company of Heroes) and the way that snipers would pick off men, machinegun nests would howl and rage, and tanks would roll thunderously through the battlefield amidst a chaotic swirling rainstorm... that atmosphere has yet to be equaled, in my opinion, never mind topped.