system stuttering

I'm running an ubuntu machine here using ltsp. For the last 2 days the system has been stuttering on a large scale. Everything will stop for a few seconds to a minute and then start moving again. top shows nothing odd. free shows that I'm using a lot of ram, but not all of it and the swap space is untouched.

Thoughts?

EDIT: I killed everyone off firefox and the situation improved. I wonder if I'm just not short on ram again. That would be a bitch. I'm not sure I have room for more and rebuilding this server would be un-cheap.