I really hate bad endings. Soul Eater got knocked down multiple levels in my opinion by the ending. Anything that makes you go read the manga to get a full story (Not Soul Eater, that's bad for a different reason) is pretty crappy. And, while I've never seen it, the infamous last two episodes of Neon Genesis Evangelion come to mind.
For one thing, yeah, having the anime end on a weird note so you
have to read the manga is pretty lame, but sometimes that happens. I think
Shaman King ended like that in the anime (I don't know yet, haven't gotten around to watching it), but considering the manga
did end up ending on a strange note anyway until it was picked back up... I'm sure there's one other show out there that did this similar to
Soul Eater... well... didn't the
Trigun anime end on a midway-point with the manga, if I read up on it correctly? Even then, the anime still had a great, satisfying conclusion, so either way, when they adapted it, they wrote it in such a way that it would end on a good note, yet keep a slight ambiguity. I personally like that in most shows if that was the style of it to begin with.
As for
Evangelion, remember, they were running on a tight budget. The last two episodes happened because of money problems, and also because I
think the networks wouldn't air the true ending (which became
End of Evangelion, and thus is a better conclusion--though some fans will tell you otherwise). Honestly, the TV ending doesn't bother me, and it was rather thought-provoking about the series. It's still a bad ending because it's more of an "easier said than done" ending, to say the least, but it does fit into the continuity of the show, in some ways. Either way, the characters remain mentally broken, one ending just has a more... disturbing take on it than the other, yet it really
does end nicely.
So sadly, there's nothing we can do if an anime has a bad ending because we have no control over the adaptation, budget, and ratings (which all come to play in some form or another). I honestly haven't run into a lot of anime that end on a bad note, and even if they did, unless the show itself was bad, they don't necessarily bother me. I mean, for one thing, I may not know of the manga to begin with (which probably helps my personal enjoyment so that way I'm not fretting over various things such as "How are they going to do such-and-such, this-and-that?"), and the other is sometimes they
do foreshadow what the ending is going to be like. Sometimes they
don't, but if it fits well-enough into that particular continuity, I'm not going to complain.
Well... the anime adaptation of
Majin Tantei Nougami Neuro ended weird, but I still enjoyed it, even if the final arc or two felt a bit out-of-place. But that's as close to a complaint I have when it comes to this sort of thing.