Episode 41 "Michael Ellis" begins with the opening theme song, followed by a screen that says "THE END," followed by the end credits, and then the show begins. This was to allow the unusual ending of that particular episode which would have been ruined by the closing credits.
In the "Royal Episode" John Cleese doesn't open with "And now for something completely different". Instead he says Queen Elizabeth II will be watching and the show begins with entirely different opening sequence and song. At the end the audience and characters stand as "God Saves the Queen" is played over end credits.
Depending on the content of the individual shows, the credits were changed accordingly, often appearing in anagrams (Tony M. Nyphot's Flying Risccu), with a different title completely (The Buzz Aldrin Show) or with strange additions to the names of the cast and crew, such as various foodstuffs, sex toys and political gambits.