From what I understand, the “evaporation” is being one with the Force in the purest fashion possible. I guess they’re consumed by the Force or something. That might explain how Jedi Masters are good at doing it. But that raises a bunch of questions, such as this happening if you overuse the Force and go too far into it, and can Sith Masters also become one with the Force? Or maybe you need to be at peace with yourself, a la Buddhism?
Huh. Now I’m curious to see what the Wookiepedia article says.
EDIT: There’s some stuff in the EU that suggests that when a Jedi’s body doesn’t disappear it means they have something else to do in the physical realm, although I think that’s a bit of a stretch. Also, I’m pretty sure there’s no connection with your body disappearing and showing up as a Force ghost, but I need to double check that.