And Red Alert 2: YR fans might find Ares [1] interesting: it's an engine-enhancement that fixes a ton of funky bugs [2] and enables loads of new functionality, and popular mods like Mental Omega and D-Day take advantage of that functionality in interesting ways.
(I used to be the lead developer of Ares for several years, the amount of reverse-engineering and C++ voodoo involved was awesome.)
I am a fan of C&C Renegade (the concept of 3D shooter and RTS gameplay is so awesome) and C&C Generals. Would love to see some community projects around them as well. Something like 0 A.D. for C&C Renegade and Generals (mind you both featured the same game engine)