Didn't get a chance to play all the games in every category (work killed me this week :() but from the ones I did play all the way through:

Mario:
Psycho Waluigi
This game highly impressed me since instead of being a typical Mario platforming clone, Thunder Dragon went one step further and went in a completely different direction with unique gameplay while at the same time being true to the roots of the franchise.

Metroid:
Project AM2R
The game has been in the works for awhile and it shows. Probably the most polished fan game I'VE EVER PLAYED! And also the fact that its a perfect remake of the original game boy game as well.

Zelda:
The Legend of Zelda: Threads of Despair
Really love the art direction and the engine is showing some promise so far.

Game of show: Psycho Waluigi
As reasons stated above, the most unique fan game at the convention and it honestly feels like a game Nintendo would of created.

Runner up:Mushroom Patrol - The Midas Machine
A Mario platformer that is highly polished while adding some creative gameplay twists without resorting to emulating Nintendo's efforts while having an original art style.

2nd runner up: Project AM2R
Most polished fan game I've ever played, nuff said.