Best:
Neon Genesis Evangelion - The End of Evangelion
Perfect way to end a great series. I loved Shinji's rejection of Third Impact at the end.
Great Teacher Onizuka
Very heartfelt finale to a meaningful, emotional series. While it could have been a bit more fleshed out, the last couple episodes was a great way for Onizuka to leave the school in a better place.
His and Her Circumstances (Manga)
A very nice ending for this manga as it balanced the humor and drama like had done the entire series. A fun epilogue made for a great ending point. It's too bad the anime never finished.
Please Teacher
A fun romcom came to a satisfying and humorous end in the last two episodes. Both emotional and funny, it was a nice cap.
Samurai Champloo
I love how casual this series ended. Similar to how it started, the three are once again on their own separate ways, but their lives are better. They seem to be happier people at the end.
Yu Yu Hakusho
I love the ending of Yu Yu Hakusho, since think it gave all of it's characters well deserved and hard earned happy endings. The final moments of the last episode makes you reflect on the journey you went on with these characters and makes you realize they are better off for the future.
Worst
B-Reaction
OK, this is a manga, and was a darn good one at that. However, it ended up being cancelled and ended abruptly. Shame.
Shaman King - Anime and Manga
The anime, which finished ahead of the manga leading to a rather lame climax, was bad enough.
The manga ending, though, made me want to pull my hair out, it felt as if the author didn't really know how to end it all and just threw together random ideas. It was a major disappointment and didn't offer any real positive closure for a series that was very up beat.