Mine:
Fullmetal Alchemist=people seem to just love this anime to death, I find the anime to be quite boring and not that interesting, while the manga is like a joy reading each new chapter. Plus Barry got screwed over in the anime

Kenshin: Just because you make one season really good, that still means 2 of them sucked.
Pokemon: While I like the anime, there was a manga that came out before it that more or less followed the games and gave it a plot, and really the anime though fun just becomes repetetitive with very little plot.
Shaman King: Big one here. They did a good job on the first 5 or so episodes, then it started to grow less and less like the manga, eventually ending up as probably the most cliched anime ever, along with horrible filler and horrible "plot twists" and filler characters. They made Faust a pansy from his awesome manga version. *sigh*
Samurai Deeper Kyo: When you turn one of the main characters from a badass babe to a whiny *not even a babe* we have a problem. The anime just gave me a headache as it went on, way too cluttered. I did like Migeira though, an anime only character.
Post yours.