Has anyone seen Monty Python and the Holy Grail? Near the end, there is a scene in which Pythons cross a bridge and in the most dramatic moment the scene is interrupted and a screen with "Intermission" written appears. It is also accompanied by music very similar to Tool's Intermission.
I know that Intermission and Jimmy are connected, but it may also be a homage to Monty Pythons. In several interviews the band says that they like Monty Python so that would make a sence.
Intermission is just an electric organ version of the first couple riffs from Jimmy, and Monty Python and the Holy Grail isn't the only movie to ever do the whole "Intermission" thing (Kung Pow: Enter the Fist for example, although it wasn't accompanied by music). But who knows? I guess it could be homage.