Red alert 2/Yuri was the pinnacle of the series.
Very well rounded game with something for everybody
Online/lan play, offline campaign, decent AI for skirmishes, and a zillion custom mods/maps/reskin/overhauls.
Generals/Zero hour a close second. I feel it did a good job of breathing some fresh air into competitive play in CnC. EA pulled support when this game was thriving, on reflection I suspect this was to "push" players onto the new titles in the franchise (which weren't as good, but were supported/updated)
CNC3/Red Alert 3 joint third. Both are good games, they just don't have the "umpth" factor of ra2/generals.