When Johnny accidentally plays footage of himself dancing in his underwear to an ABBA song on live international television.
Pegasus: Everything in order, English? Johnny English: I think you'll find it's rather more than just in order, Sir. You are now entering the most secure place in the whole of England. [the most secure place in the whole of England explodes]
The sequence where English pretends to confront and defeat a (non-existent) assailant, to shift the blame from himself after knocking out a man with a wine bottle. Following that up is when he "describes" the assailant to a profiler, using only a fruit bowl as inspiration (see the main page quote). Then there's the "assailant"'s Brick Joke appearance in the credits.
Johnny starts dancing to Cameo's Word Up right in the middle of assassinating the Chinese PM when Tucker interrupts Simon's command with a Montreaux radio station. The WTF reactions are understandably hilarious.