Hero
Best: Iron Man. One of the most interesting characters in comics at the moment. And yes, he's still a hero.
Worst: Wolverine. I'm a big fan of the character, but 2006 was not a quality year for him. Far from it in fact.
Villain
Best: Vanessa Fisk.
Spoiler:
The whole attempted murder of Foggy, manipulating Murdock with Karen's scent etc etc etc. Basically psycologically mind****ing Daredevil. Great stuff.
Worst: Vulcan. Don't care for this character in the least. Especially as a villain.
Team
Best: X-Factor
Worst: Not sure...
Fight
Best: New Avengers vs. Super Adaptoid. New Avengers Annual #1.
Worst: Namor vs. Wolverine. Wolverine #45.
Cliffhanger
Best: Runaways #22.
Worst: Not sure...
Writer
Best: Chritos Gage and Brian K Vaughn.
Worst: Loeb.
Artist
Best: Mcniven.
Worst: Humberto Ramos.
Writer/artist combination
Best: Brubaker and Epting.
Worst: Loeb and Leifeld
Cover art
Best: Del'Otto
Worst: Leifeld
New series
Best: Iron Fist
Worst: Not sure...
Miniseries
Best: The Escapists
Worst: Onslaught Reborn
Single issue
Best: Iron Man/Captain America: Casualties of War.
Worst: Wolverine #45.
Graphic novel
Best: The Fountain
Wost: Not sure...
Event or crossover
Best: Civil War.
Worst: Dunno...
Overall ongoing comic
Best: Y: The Last Man and Daredevil.
Worst: Black Panther.