I'm rather oriented on second half/late 90', but definitelly RTS games from this period are something I have nice memories
Definitelly Starcraft + Brood war and Warcraft II (Battle.Net edition). Both KKND games, but in terms of campaign I prefer a bit more first one (probably due to cut-scenes, which were a bit more dynamic and interesting).
I like a lot Dune 2000, as well as Red Alert 2 and Emperor: Battle for Dune (but these two are rather not counting to 90' period). I appreciate Red Alert 1 for interesting, more "mature" profile, as well as the fact that they've shown Stalin very accurately, as genocidal murderer, but in terms of gameplay... Well, it's a bit tough cookie, plus I need to play in it (as well as in Dune 2000) in rather low resolution (playing in high resolution in OpenRA or Gruntsmod is causing that I'm playing with army of ants - my eyes literally hurts me).
I've enjoyed a lot Seven Kingdoms when I've finally learned how to play in it (training in SK II was made in very weird way - you're automatically tranferred to training with playing as Fryhtan's, completely skipping training for playing as humans, options for human's training are somehow "hidden", good thing that first game is showing well how to play as humans, since there wasn't introduced possibility to play as Fryhtans.
Don't know if I can count it as RTS, but I liked also Myth 1 and 2, as well as Small Soldiers game.