The way Basil's housekeeper reacts to him shooting the pillows
Housekeeper: (helplessly) My good pillows! Mr. Basil!
Basil: [peers over back of chair with a slightly wide-eyed look on his face]
"It will be most dangerous." *Accidentally sits on violin*
"It was my fond hope to stay and witness your final scene, but you were fifteen minutes late.."
When Basil is gearing Toby up for searching out Fidget. The whole time Toby is growling and looking angry. Then THIS happens:
Basil: Low brow, close set eyes, broken wing-
Toby: [once the last one is mentioned, he looks at Basil with a look of clear confusion]
Basil: Oh, he's a peg-legged bat with a broken wing.
In an instant, he's back to growling angrily.
"I love it when I'm nasty."
Even Felicia gets one, when Ratigan orders her to spit Fidget out. The grumpy "You're no fun at all." expression right before she does so is pretty priceless, as is the rather moth-eaten state that Fidget comes out in.
She gets another one earlier in the movie, right after she eats Bartholomew. Ratigan asks her if she enjoyed her meal, and she burps in his face. The look on his face is hilarious.
"Item 96: A heavy tax shall be levied against all parasites and spongers. Such as the elderly. The infirm! And especially (hee, hee) little children."
There's a storybook adaptation where this is the only line from the movie that is used in the book.
Twice in a short time span Basil gets an absolutely ridiculous dazed look on his face—the first is when Toby, in his hurry to rush off on Fidget's trail, steps on his master; the second in the toy shop when he gets his head smashed between a pair of mechanical cymbals.