I don't think there is a RTS I haven't played over the years... Nothing brings more fond memories than original Dune. But for competitive play with friends, Supreme Commander 1 and 2 are my favs.
ahhh Dune, that was so much fun. Nothing like a sandworm eating your tank rush.... Z was another good RTS from that era, good combat and some great FMV sequences
Tiberian Sun and Age of Mythology are my favourites. I wish I could go back in time to play the other RTS games like Empire Earth and Rise of Nations. Better still, a game studio should make new RTS games so we can stop obsessing over the 1990s. I don't care much for the new Halo Wars, it's all about multiplayer and it probably has no story line.
Back then it was the age of RTS games in PC. Now most PC games are either MOBA or cross platform. RTS means PC only. MP is the only way to make money.
Homeworld. All three (1, Cataclysm and 2).
Why? Persistent fleet, full 3D movement and some of the best storytelling - not just in RTS - but in gaming.
While I like HW for its uniqueness, the Command and Conquer series is the most fun I've had playing the genre with friends. Particularly RA2 and Generals (yes, it isn't a part of the main series, but still great). What makes them great is that they're relatively easy to jump into compared to something like Starcraft.
Warcraft II - I remember trying to get multiplayer working over dial-up with my brother. Warcraft III followed and we still play it today at LAN parties. Oh, and it just happened to spawn the most successful MMORPG game in history