Parker and Stone did, in fact, do a "Mohammed" episode but they didn't go any further than putting Mohammed in a bear suit or something because they didn't want to actually draw Mohammed and get in trouble with the islamists. That was supposed to be the big joke of the episode, that they couldn't/wouldn't actually show Mohammed. Big deal.
As tame as it was, Comedy Central banned the episode from their website, though, so I can't link to it. Such cowards.