The scene where Wallace and Gromit try to dispose of the bomb, but can't because there are ducks in a pond out of one window and nuns through another is a reference to the scene in Batman (1966), where Batman, played by Adam West, has similar problems whilst trying to dispose of a bomb.
Early in the film when Wallace is attempting to save Piella, they enter a zoo with a number of posters near the front entrance. One of the posters on the right side is of a 'lost penguin' similar to the one of Feathers McGraw seen in The Wrong Trousers (1993). In the same scene, a ladder can be seen propped up against the inside of the wall to the left of the gate; dangling from it (outside the wall of course) is a rope made from sheets knotted together. This means he has escaped from the Zoo and is presumably still at large.
Albums in the filing cabinet at the end of the film include "The Hound of Music" and one by a group called "The Beagles" written in a font similar to that used for The Beatles "A Hard Days Night" or "Help", and two by "McFlea" (McFly).
Fluffles owns a single by "Doggy Osmond," a parody of singer Donny Osmond, whose 1971 hit single "Puppy Love" has become his trademark. The lyric "and they called it Puppy Love..." can also be heard sung at the end of the film.
The trivia items below may give away important plot points.
In the final battle between Fluffles and Piella, Fluffles appears in silhouette in the lifter suit in a similar fashion as Sigourney Weaver did in the movie Aliens when fighting the Xenomorph Queen. Also, the ensuing fight between Fluffles and Piella is very reminiscent of that of Aliens.