Plan 9 From Outer Space is referenced in the Movementarians' training film - the string on the model UFO is visible, bearing likeness to the one in the movie.
Homer sings the theme tune with the word "fishing" in place of "Batman". Later it is sung again with "Leader" as the word, except on the last one Homer gets it wrong and shouts "Batman!... I mean leader!"
Willie scratching his nails along the church window to get Marge and Reverend Lovejoy's attention is a reference to Jaws, in which the character Quint performs a similar action.