I never did play Dune II, but I did download the first Command and Conquer: Red Alert last year when it was released as freeware. If you have fond memories of the game, I suggest you don't look for it.
The RTS genre just does not age well. I even have trouble playing the original StarCraft due to the horrible resolution, lack of auto-mining, and total fog of war in multiplayer.
Yeah I'll agree with you about Command & Conquer. Other than Red Alert 2 I hardly ever play the older C&Cs anymore. RA2 just had the right mix of modern(ish) features and old school graphics to keep it fun for longer than five minutes, something I can't say for the older games anymore.
StarCraft on the other hand I still play pretty regularly, the game still plays pretty much exactly the same as StarCraft II, minus the horrendous load times between missions!