What are you doing on the machine? Are you working it very hard? In particular, are you working the hard drive very much? Something like a file sharing app can make the temperatures rise as it constantly reads and writes to the hard disk.
Well, there's a
hack you can install to use clamshell mode on an iBook but I strongly recommend you don't, particularly if you're finding the machine's running hot in normal mode. A lot of the iBook's heat is dissipated through the keyboard so the clamshell hack can sometimes cause the iBook to overheat.
Having said that, it can be perfectly safe if you don't do anything too intensive.