Valves, wrist pins, clutch, stator, shift segment, hd oil kit (Sean's, I don't know about the PCW one), flywheel... I'm sure there's more. It seems like the only reason you HAVE to pull the motor is to split the cases. A lot of the other stuff is way easier with the motor out, though.
I know the front head can come off with the engine in the frame. The manual says to pull it for everything that's tricky, but most things seem to be possible if you're willing to bear some busted knuckles.
Things I know that you HAVE to pull the motor are transmission work and crank stuff. Those require splitting the case.