Warzone 2100 is a great game, I'll concede quite happily. However, it's not my fave at the moment. (Although I AM one day starting an organization named 'The New Paradigm' and I'm using the logo from that game. )

I think my fave at the moment would have to be either Command & Conquer Red Alert 2 (With Yuri's Revenge.), or Starcraft (With Brood War). Both of these games are excellent examples of how the genre ought to be done, and the fact I not only still play them but rate them so highly after all this time shows their excellence.

Empire Earth II would be there, but something about it seems hollow. I don't know... it just lacks the epic feel of the original for some reason. I can't put my finger on it. If it had that, I daresay I'd rate it as one of the best though; technically it's all good, and everything fits together pretty well.