Sorry, no episode numbers, though I could give estimations... ^^;
Well, anyway, I've read this thread before but never got around to actually answering the questions myself... and since I have free-time today, I will! ^_^
Though I'll probably have multiple answers...
-Best fight scenes overall
Sasuke vs. Orochimaru (Chuunin exam) was awesome to watch
Lee vs Gaara (Chuunin exam) well, LEE was awesome to watch. Gaara kinda just stood there...
The Sannin fight - I loved watching Tsunade slap Orochimaru around
Lee vs. Kimimaru - Kimimaru's movements and Lee drunk. Yah, awesome.
Sasuke vs. Naruto (Valley of the End) kinda goes without saying..
-Best Naru/Sas fights against eachother and together (against a villan)
the fight with Haku. I really loved that, because Sasuke was fighting and protecting Naruto. And then Naruto when all kyuubi. This was the starting mark of something great.
-Best Naru/Hinata moments
Just before the Naruto vs. Neji battle, and Hinata pushed aside her shyness and talked to Naruto from her heart. ^^ It was very sweet and I loved what Hinata had to say about Naruto. They're meant for each other.
-Best Naru/Sakura moments
It's more recent, in the manga, when we see them again and both get all depressed when Kakashi mentions Sasuke. XD It made me laugh. Also, when Sakura told him about the cursed seal (before Sasuke left).
-Coolest jutsu (and by whom)
All of Neji's attacks are rather awesome. I also like Sasuke's attacks. ^^ Ask me their names and I'll laugh, because I don't remember.
-Most vicious Villan (try to differ on this one from the other posters)
Uh... Orochimaru and Itachi, without even thinking. But to dig a little deeper - Gaara's father.
Kakashi, of course.
And here's some of my own:
Sasuke and Sakura for starters.
Naruto and Hinata or Kiba and Hinata (though I prefer her with Naruto)
Shikamaru with either Ino or Temari (though I prefer him with Ino) ^^
-Least Favorite Couple(s)
Sasuke with Naruto or Itachi
Sakura with Naruto or Kakashi or Itachi
-Best Opening Theme
Haruka Kanata, Fighting Dreamers(?), and I like the filler's opening theme though I don't know the name...
-Best Ending Theme
Parade and Wind