All of the running gags, like Changed Daily's different names and Professor Professor's "Victor, ARE YOU STILL ALIVE!"
In "Alien Attack", Victor realises that he needs to save the world with a taskforce of vegetarians. Problem is that all of them except for Victor himself happen to eat fish too, and thus are actually pescetarian.
The ending to "Secret Double Agent", where a sobbing Kent, who was believed to have performed exceptionally well (but was really just working poorly for T.H.E.M.), receives a medal and is made the chief guard of the Secret Thing. He then proceeds to laugh evilly.