I didn't read a couple of the pages on here, but some of the more random obscure ones I can think about that made me pop a blood vessel:
Chrno Crusade - I fell in love with this series, despite its shortness and horrible historical inaccuracies ((ffffffffuuuuuuu)). It's short, but there was a nice story being told in the manga and even if it was understated, a lot of depth was given to most of the main cast (and villain).
The anime was a big steaming pile of fanservice shit. To be fair, it was another victim of an anime being made from a manga that only 1/3rd of it had been published prior to the anime's creation. It went off in a crazy direction, and turned the villain into a creeping, rapist-like character who was truly rotten to the core… something the manga clearly stated that he wasn't. Despite the suddenness, the manga wrapped up the story completely, but there was a lot of loose ends and bullshittery going on at the end of the anime. Plus the deaths of Chrno and Rosette in the anime was so fucking cliche I still can't.
Getbackers - This is not a masterpiece by any means, but in the second half of the manga, a very complex story begins to unfold... something on an entirely different level then what came out of the anime. The anime really didn't even get to cover the entire first half of the series, as its mostly full of filler shenanigans and more yaoi fanservice then you can shake a stick at.
Sometimes the story and "what is the fucking point of this show" feels get so high while watching (or even reading the first half of the manga) this anime its really hard to enjoy... it does all get wrapped up by the end of the manga, and the drama and highs and intrigue are exceptionally high and good. I'm pretty sure the manga finished long after the anime did.. It would've been nicer if they had done a 50 episode series that came from the entire series.. without all the filler nonsense and proper pacing, it would've made for a more interesting watch.
I also agree with what people have posted about Negima, Rurouni Kenshin, and especially Trigun >___> And the original Hellsing anime, but the OVA rectified all of its sins, completely.
I know I'm missing something, but Chrno Crusade is the one that makes me blow so many gaskets.
And though its not horrible, the unnecessary plot changes and love triangle they did/added to the second season of Emma: A Victorian Romance made me seethe to the core. I have nearly worn out my manga copies because I have read them so many times, this series is one of my truest loves. Though again, I don't think the entire series had been completely yet... but a lot of the stuff they changed and messed around WAS done and published prior to the creation of season 2 >_>