FLCL and that one other anime I know of but can't remember... Ninja Nonsense I think? That was the english title. The original one was like 2x2 Shinobu or something. Both were 6 episodes long.
The shortest anime I know is "On your mark" made by Studio Ghibli. It lasts c.a 10 or 5 minutes, there are no dialogues, only a nice song is playing all the time. When I first saw it on YouTube I thought it's some fanmade AMV, but later I found out it's an anime. It's about two soldiers who saved an angel girl.
There are a bunch of hentai series made by this one company. Don't know what the studio is but they are all or at least a majority are two episodes long. I haven't watched them myself. Wikipedia takes you to some strange places when you decide to just start clicking.