Tough choice. I agree with many of the others on this thread that the list should probably be longer.
If I had to choose, I'd say:
1) Spiderman
2) Batman
3) X-Men
I liked the animation on Spiderman. Batman had better writing, but I didn't like how they drew Batman to look like Jay Leno on steroids. X-Men had some good animation and some good writing, but they kinda screwed the pooch with their "non-violent" action (Wolverine couldn't even use his claws, except for against inanimate objects and sentinels).