Well, Total Annihilation and AoE2 would definitely be jostling it out for runner-up. For a sci fi game, TA was fantastic at simulating naval warfare, air operations, combined arms etc, and the huge pop cap was great. AOE2 was just an incredibly polished game, with all the different buildings matching particular ethnic architecture. I learned so much medieval history just from reading the manual.
But, I just can't go past the original Company of Heroes for my favourite ever.
-Resources being tied to capturing territory rather than peon micro means the game is so much more tactical. There's nothing like the feeling of gearing up to make a push on the enemy line so you can take back the VP or fuel point.
-Lots of little touches: cover, dropped weapons, buildings that can be garrisoned and destroyed, wrecked vehicles that can be salvaged or used as cover, detailed sounds from different units, being able to lay defences like wire, sandbags etc
-The AI was better than any game I've played. It shows its age now, but the AI was leaps and bounds ahead of what had been done at the time. Even now, if you set up a massive defensive line, the AI will figure out where the weakest spot is and attack right there.
-It just gets the feel and balance of a WW2 game exactly right. Infantry and support weapons dominate the battle for territory in the early game, before light vehicles come out to try and push the infantry off, and finally tanks hit the field. Each time that happens the balance is completely shaken up and you have to react quickly.