I won't go into a discussion about naruto, bleach, and inuyasha but I rarely see people talk about Getbackers(awesome manga) or Cowboy Bebop(classic in pretty much every way).
^.^ since i've got some time, heres my favorite, by category
Action: Samurai X(original movie, not the ruro-ken one)
Comedy: Sayonara Zetsoubo Sensei
Romance: Welcome to the NHK
Fighting: Tenjou Tenge(still prefer the manga)
Classic: Ruro-Ken(first two seasons)
Shonen: One-piece(fuck naruto and bleach)
Shoujo: Darker than black(I kinda have a hard time believing shojou made this)
Now i rly judge all anime pretty equal, but these are the less popular ones i find not many ppl watch. I pretty much judge anime this way:
1. Style:is it a HQ anime. Example: Bakemontegari
2. Storyline: Does it follow the manga, or even, is it a good story. Example:Berserk
3. Ending: for those that have ended, does it give closure. Example: Code Geass(you may not like the ending, but it resolved everything.)
4. # of episodes. Does it simply waste airtime for money(naruto and bleach) or does it do it for the sake of entertainment. Example: Hellsing OVA.