Starcraft, nuff said.
2. Total Annihilation
The first rts to feature 3d units and structures and truly massive armies and bases. The units were all basically a nerds fantasy come to life; a combination of Transformers and Mech Warrior.
Your buildings transformed every time they made something. You had guns that could fire across maps and robots so big they could walk on and crush other robots.
3. Command & Conquer: Red Alert
While the original essentially created the genre Red Alert featured a game spanning sense of humor rarely seen in a genre that often takes itself way too seriously.
4. Warhammer 40,000: Dawn of War - Dark Crusade
Starcraft 2 before Starcraft 2, brilliant and addictive gameplay with a visual style and atmosphere that represented the 40k universe better than any other game prior.
5. Warhammer 40,000: Dawn of War II
The most innovate rts single player gameplay made to date, playing more like an rpg with the added awesome-ness of co-op. If only the multiplayer were as good as the originals it would have been a true masterpiece of rts gaming. Once again Relic prove they are the masters of the 40k universe. Also Tyranids.
6. Warcraft III: Reign of Chaos
Warcraft 3 has been modded so much that an entire sub-genre emerged from its community starting from a single map called Defense of the Ancients. The game itself was pretty traditional but featured restrained unit counts and special hero units that functioned like rpg characters and probably served as the foundation along with Diablo for World of Warcraft.
The story also remains one of the best most memorable game stories ever told and its an RTS!
7. Supreme Commander
Total Annihilation 2 but with a different name for legal reasons. Modern graphics and insane unit counts with every single aspect of gameplay being simulated in real time made this one of the single most cpu intensive games ever made and still chugs on the best of best hardware during the 1000 vs 1000 unit cap maps with 30 square kilometers of battlefield. It can literally take you half an hour to get some units from one side of a map to the other.
8. MechCommander 2
Mech Commander 2 was one of the most under-appreciated funnest games of all time on PC. The first rts to truly do things differently where bases were done away with and all you had to care about was how much ass your were kicking with your 10 to 20 walking death machines of which you could customize their entire weapons load out. One of the greatest crimes of gaming is how few games have been set in the Battletech universe.
9. Metal Fatigue
Basically Starcraft but with giant Anime-esc robots. You could customize your robots torso, legs and arms, choosing between a diverse range of weapons from missile legs to giant buzz saw arms to emp torsos. It was simple amazing fun and it sucks that it was the last game Psynosis ever made. The game featured level design never seen before in an rts with both land, sub-terrain and atmospheric battlefields, all of which could be seemlessly transitioned between.
Also the cgi intro is bad ass. I actually remember it word for word I watched it so many times over.
10. Dark Reign: The Future of War
One of the all time greats that never got the praise and attention it deserved due to existing in a time when Starcraft was still the king of the genre. This game had some of the best AI design behavior ever to exist in a game. You could specify what types of actions to take in unique situations for every single unit under your control all just by pressing a handful of buttons. The unit designs I recall were especially cool, like spider bikes. Freaking SPIDER BIKES!