The historical figures' oral presentation. Most notably, Ted calls out on Napoleon's strategy (regarding the use of a "Water-slide" aka Waterloo)
Bill and Ted bringing Beethoven with them. They come up to him while he's playing, and when he won't listen to them, they just up and carry him off the piano. He was so distracted, he was playing, well... air piano.note While it is known that Beethoven had become almost completely deaf towards his final years - he died in 1827 - The Other Wiki points out that he could still hear music normally by 1814, and the film states outright that B&T brought him from 1812. So this can be easily chalked up to distraction, or pure Rule of Funny.
Sigmund Freud vs. the police examiner:
Interrogator: Look, I want to know why you claim to be Sigmund Freud.
Freud: Why do you insist I'm not Sigmund Freud?
Interrogator: Why do you keep asking me these questions?
Freud(leans forward): Tell me about your mother.
Camera shifts elsewhere.
Freud: Would you like a couch to lie on?
Interrogator: No, I do not want a couch to lie on!
Bill & Ted's Bogus Journey
Bill and Ted explaining why their girlfriends/fellow band members are able to play better than they themselves.
Death to the smoker at the hardware store: "See you real soon."
From the Spinning Paper Montage: 'Death Wins Indy 500; "I didn't know I could run that fast."'
B&T Melvining Death, of course. Made even funnier in the comic adaptation with this follow-up.
Ted: Death wears funny shorts.
The Good Robot Usses decapitating the Evil Robot Usses is funny in itself, but the fact that the Evil Robot Usses are so nonchalant about it makes it hilarious.
Evil Robot Bill & Ted: Well played, human usses!
De Nomolos's Mooks seizing control of a room using typical action-movie-thug poses and body language, dressed in standard-issue paramilitary black ... and giant floppy black boots made of polyethylene foam, which are apparently all the rage in their time.