"Super Best Friends" was removed from the South Park website and Netflix instant streaming because it included a depiction of Muhammad. Later, in Cartoon Wars: Part 1 (2006), South Park Studios created a similar plot with Family Guy (1999), when really, it happened to South Park in real life.
Kenny's uncovered face has, to date (August 2007), been shown four times on the show. This is one of the four episodes.
While Jesus and Friends are watching the giant monitor, their reflection in the glass floor shows a Visitor.
Meanwhile, at the White House, after the scene in which the Blaintologists are instructed how to drown themselves, George W. Bush is shown looking down and commenting on the situation. Before this scene ends, his next door neighbor Larry pops in and says "Hey George! What's going on?". This is a reference to That's My Bush! (2001) created by Trey Parker and Matt Stone.
The Center for Magic is identical to the Waco, Texas compound from 1993.