Gah, this is really hard, so I'm going to only list one of my favorites for each category (categories decided based entirely on how I can justify portioning out some of my favorites).
1. Book (Singular)
American Gods -Niel Gaiman
2. Book Series
The Book of the New Sun -Gene Wolfe
3. Young Adult Book Series
The Bartimaeus Trilogy
4. Comic/Graphic Novel (American)
Transmetropolitan -Warren Ellis
5. Manga
One Piece
6. Anime
It would be cheating to put any Miyazaki, but... Kiki's Delivery Service
7. Television Series
Doctor Who
8. Film Series
Toy Story
9. Film (Singular)
The Princess Bride
10. Theater Production
Wicked