Trinity Blood, since it kind of had no ending, it only left quesitons unanswered and the main antagonist still alive and at larger. It even brought about a flood of new questions, besides the ones they never answered.
Also Inuyasa the Anime went directly off the manga, and the manga is still going and from the looks of it, it's reaching the end.
@haruka - I hated the FMA movie ending, sure the brothers are back together but everyone they love is on the other side of the gate. Also even if they only need each other to be happy, there is a person left behind that needs them, Winry. She has feelings for Ed which you can tell even though it is not stated clearly, and Ed n Al were basicly the only family she had besides the old lady.