I'd take a bullet or two for Total Annihilation: A C&C clone, perhaps, but probably the most shining example of a C&C clone out there. Yes, the gameplay was sluggish, the AI was terrible, and the multiplayer was buggy and difficult to work with, but it had a ton of interesting and unique units and structures, the ability to create custom units, a campaign that required some serious tactical thinking and the first example of a super unit in a strategy game: the Krogoth.
I'd also go out on a limb for Quake II. It had a single player campaign whose level design still compares favorably to most modern shooters, a great variety of weapons, and REALLY ADDICTIVE MULTIPLAYER. It was also the last shooter I know of to let players import their own custom character models for use in multiplayer, which I thought was really cool.