go go go go go
For me, it would have to be 神様のメモ帳 (Heaven's/God's Memo Pad), mainly due to the fact that it actually brought me to tears with the end-of-series twist. Steins;Gate is a very close second for me, but I found God's Memo Pad to just efficiently wrap everything up well while still retaining a lot of detail and emotion in half the time that Steins;Gate did.
I'd have to give a notable place to Boku wa Tomodachi ga Sukunai also. Even though it's a comedy and pretty fanservice-y, the underlying story between two of the main characters is really quite emotional, and the ending to the series ties it up wonderfully.