I had one of my best birthdays ever playing through Subspace Emissary. As an actual multiplayer Smash game, it's clearly the worst one. As a big dumb crossover? It's everything I ever wanted.
Not quite as hot as the legendary Symphonia, but there are people who would beat me up for saying that. The story is great most of the way through, but starts to fall apart a bit near the end.
Arkham Asylum kicks ass. There are plenty of licensed super hero games that serve as showcases for the chosen IP, but Arkham Asylum really makes the most of its source material and hits the player in the face with everything that makes Batman good.