The top 3 that come to mind are:
Command and Conquer Red Alert 2 (PC) ; in my opinion the last good C&C game. Only private servers are available now and even those are diminishing..
Phantasy Star Universe (Xbox360): Even though there's that one time of the day with alot of people, occasionally you'll find yourself completely alone...
Too Human (Xbox360): Alot of people have various opinions on this game, but I absolutely loved it, can't find a single person to co-op with these days because its a couple of years old..