Obviously there'll be major spoilers in this post as well.
Clannad ~After Story~: This has easily been one of the most controversial endings I've seen from any anime. It pretty much implemented a fantasy reset button at the end to nullify everything that happened in the past few episodes, bringing Nagisa back alive after her depressing death. And those episodes were just so damn emotional...I couldn't stop crying. They just did so much...emotionally, character-wise, etc. So for it to end the way it did, I felt almost betrayed that it made me go through that experience when everything was going to be alright in the end. I know some people argue that it was only following the visual novel (where the ending works much better due to game mechanics) and there was foreshadowing, so it was a total deus ex machina, but I still hated it. The only thing it really got right was the tone...the show was meant to end happily, but the situation it put itself in just really pissed me off.
Death Note: Actually, the ending was solid, an emotional death for Light. It's just that the way it lead up to that conclusion didn't seem quite plausible given Light's prudence. Well, in general the series went downhill after L's death anyway.
Kuragehime: It was a pretty solid show so the ending didn't affect me as much as the other other two, but the way it ended...it wasn't really an ending at all. There were still many loose ends to be tied but it just sort of ended abruptly. Probably could've used a few more episodes to flesh out a better ending.
Arakawa Under the Bridge x Bridge: The first season had an ambitious premise with its oddball romance, and I was hoping to see a little more character development with Nino. Unfortunately, they tease us in the second season with the whole "Trip to Venus" storyline, but for some reason, the producers decided to never resolve it. In fact, they completely disregard and replace it with something totally random.
Welcome to the NHK: The ending was just...dull. I expected more analysis into the psychotic mind towards the end of the series but it never delivered. Barely felt like an ending to be honest.