Yesterday a user asked me about a Java application that was unusably slow when running over SSH X forwarding. This was using Ubuntu 12.04 + Unity; weird thing was, it was fast on a laptop that was also running Ubuntu 12.04 + Unity. Other X apps were fine over SSH to the same host.
Turns out there are a lot of complaints about Java applications being slow over SSH. This bug in particular looks likely. If I read this bug correctly it's been fixed in 12, so I'm not sure why I'm seeing it. There were some differences in packages between the laptop and the desktop, but nothing jumped out; both were using NVidia graphics + the proprietary drivers.
In the end, a workaround was to use i3, a spartan (but oh so good) window manager. Interestingly, the app showed faster performance under XFCE than Unity, but not as fast as i3. Maybe a problem in a couple of different libraries?