The way Basil's housekeeper reacts to him shooting the pillows
Housekeeper: (helplessly) My good pillows! Mr. Basil! *Spits up a feather*
Basil: [peers over back of chair with a slightly wide-eyed look on his face]
"It will be quite dangerous." *Accidentally sits on violin, followed by a stream of Angrish*
"It was my fond hope to stay and witness your final scene, but you were fifteen minutes late.."
"Heheh...hahaHA, yes! We'll SET THE TRAP OFF NOW!"
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.
Basil trying and failing to get Toby to sit, until...
Olivia: Sit, Toby!
Toby immediately sits.
"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.
The way Dawson just pouts after yelling at Basil for giving up while they're stuck in the death trap.
During the Let Me Be Good to You segment, Basil's look of utter exasperation after Dawson gets up and dances with the girl mice.
Bartholomew: To Ratigan, the world's greatest rat!
(Ratigan proceeds to take a Spit Take, while his cronies look in horror)
Ratigan: What was THAT?!
Ratigan: WHAT did you call me?
Thug 1: He didn't mean it professor!
Bill the Lizard: It was just a slip of the tongue!
Ratigan: I AM NOT A RAT!
Thug 2: 'Course you're not! You're a mouse!
Thug 1: Yeah, that's right, right, a mouse!
Bill the Lizard: Yeah, a...a big mouse!
Ratigan's very festive reception of Basil "getting the drop on him"; balloons, streamers, confetti and a big poster with "SURPRISE!" written on it in massive letters.
The fact that Ratigan went to the trouble of writing a song, hiring a band to record it, finding a means to record it and get it pressed onto a record, in addition to his elaborate Rube Goldberg Device trap, just so that he can rub Basil's nose in his success.