My favorites would be...

Best character: I love Shikamaru because of his attitude and the fact that he represents someone who uses their head to win absurdly dangerous battles, which is what sets Naruto apart from typical 'power up and fight head on' shounen series like DBZ or Bleach. I'm glad that he developed greatly with Asuma's death. Also, the 'lazy genius' is just great.
Also: Sai (moreso before he 'saw the light'), Kabuto (always shows up at the most surprising times)

Best Element: Power != Victory. Sure, every now and then someone will get by based only on their special ability or sheer strength or whatever, but the series hinges greatly on planning and thinking. Shikamaru can beat Hidan, Deidara can come absolutely damn close to killing Sasuke (and does beat Gaara), etc.

Best Fight: I'm a sucker for how they do the Rock Lee taijutsu fights in the anime, but in the manga, I'm not sure... The battle of wits, again, are what really get me hyped up. As probably guessed, I love almost all the fights with Shikamaru in them, although the battle at the bridge was pretty spectacular also...

Best Jutsu: I don't know what beats the Mangekyou Sharingan, but my favorite jutsu so far is Gaara's special sand abilities. Outside of bloodline limits, I'd have to go with good-old Kawarimi X Henge combo, a time tested escape and feint move that is key in many battles and strategies.

Best Story: Gaara's backstory is just amazing. I also really enjoyed the student-teacher connection between Asuma and Shikamaru.

Best Comedic Moment: Can't decide. Konohamaru's yaoi-no-jutsu and yuri-no-jutsu were really funny to me, but I also like the interaction between Sasuke's new teammembers.

yeah, my two cents...