Oh, geez, there are so many...
The rat farm is definitely a classic, with Peter as the overseer
Fat Stewie (Brian: Awww...Orson fall down?)
Peter and Barney Rubble
Stewie invading Mister Rogers Neighborhood
Stewie as King Friday
Wrong-sounding Muppets
Kermit in the swamp with a shotgun
Stewie on "Kids Say the Darndest Things"
Brian joining the police force and becoming addicted to "white powder"
Peter turns the house into a giant puppet
Peter turns a room into Pee-wee's Playhouse
Peter, Chris, Stewie and Brian vomiting after drinking ipicac
Stewie executing the vaudeville guys
Cookie Monster in rehab
Stewie's Blues Brothers reference: "Got my Cheeze Wiz, boy?"
Anything involving Herbert - I dunno, he just makes me laugh
Stewie beating up Brian, because Brian is late paying back a debt he owes Stewie
Peter and the Giant Chicken in their longest fight to date...they stop midway and wonder why they are fighting; they can't remember, and we next see Peter, the Chicken and the Chicken's wife at a fancy restaurant; Peter and the Chicken argue over who gets to pay the check, and the fight resumes
Isaac from "Love Boat" shot by Abraham Lincoln
Stewie introducing John Lennon to Yoko Ono: "Don't make me do to you what I did to John Lennon!"
How Joe became handicapped (he fell off the roof of a house while fighting a Grinch-like creature)
Peter turning into a giant blob
Mr. Weed's death
There are a LOT more, but these immediately come to mind.