I almost started crying when Gungrave turned into the "superiors" and "beyond the grave" crap. That could have easily become one of my all time favorites.

PMK, in my opinion, was already ruined by the fact that it didn't really have much of a story.

Cowboy Bebop had the supernatural "pudding" attacking people episode... but that was only one episode, and I would'nt call cowboy bebop a "good" show in the first place either.

Berserk - I would've much preferred if berserk remained a simple down to earth medival fighting anime. (yes I realize how dumb that sounds since the manga has volumes upon volumes of supernatural stuff.. Its just that the anime made it seem like it could've been a non-supernatural series) I wouldn't call this series ruined though.. its one of my all time favorites.

UC Gundam - (Zeta, Victory, CCA) Some might argue with me and say that the newtype miracles are purely science fiction (since newtypes are supposed to be the next step in human evolution), but I'll put this here anyways. Seeing ghost powered mobile suits, or people communicating with ghosts, or people moving large asteriod sized objects, etc.. hurt the series. There were plenty of other problems with these series/movie, and having these newtype incidents certainly didn't help.

Evangelion - I dont think I need to say anything here. It might actually have been a decent story with mechs fighing angels... but... well.. you guys know what happened to it.