Not since the big Mohammed cartoon riots. Then they specifically took that on and tried to show him but the networks wouldn't let them. Then they did something very unflattering with Jesus to basically make the point "Why does the network allow us to do this with Jesus, and we can't even show Mohammed in an average situation?"
Actually, they have never made fun of the muslim religion. It’s funny that even we conservatives have become so sensitized that we are praising them for even SHOWING A PICTURE OF MOHAMAD (in the superbestfriends episode), and calling them brave for trying to show mohomed buying tea.
Imagine if they did an episode of the prophet beating up his pre-teen wife. Then I’d praise them for their bravery (probably at their funeral).