I love Dune II. It's still my most favourite RTS game until today and that's mainly because I played it in 1993, soon after its release. As Dune II was one of the first RTS games ever created, I hadn't played anything like it before. The game mechanics felt so fresh and different from anything else, it blew me away and the new RTS genre became one of my favourites.
For me the Dune franchise doesn't count as RTS series though, as only Dune II became a classic (the first Dune wasn't a RTS game, Dune 2000 was just a Dune II remake, Emperor: Battle for Dune seems to be a game not only I haven't played).
So from the franchises listed my vote goes to Age of Empires as like the series a bit more than Warcraft and much more than C&C.
For some reason I never really liked Starcraft and never finished it. There, I said it.
I want to mention one series though (if we can call the two games a series), which I like even more than AoE and Warcraft and which comes very close to Dune II in my RTS ranking: Dungeon Keeper.
