This is a rather difficult thing to narrow down. Joust was the first game to spark my interest in co-op. Contra and River City Ransom solidified it. My favorite though, would have to be the one that creates the best co-op experiance. And that is Monster Hunter Tri.
I could list all the "co-op features". Split-screen. Matchmaking. But none of that matters really. What matters is the feeling of acomplishment and camaraderie when you and three of your friends take down a beast that could possibly have eaten you without even chewing. Most importantly, it can take 4 complete strangers and turn them into a team.