The ending where Thomas o'Malley becomes a father with Duchess and the kittens.
Thomas o'Malley,The Alleycats, and Roquefort rescuing the cats. Special mention goes to the scene where Thomas and the Alleycats start attacking Edgar while Roquefort is trying to rescue the cats from the locked chest.
Marie's interaction with Duchess throughout the film. Sure she may be a bit spoiled and a "tattletale" according to Berlioz. But she has a very close relationship with her mother throughout the film especially in the "Scales And Arpeggios" scene.