Season 11 of the Simpsons: BABF01 (Treehouse of Horror X)
A global "Y2K" meltdown destroys earth after Homer neglects to debug the Springfield Nuclear Power Plant's computers. A rocket is headed to Mars and a lot of stars go aboard. Including Paul McCartney! (he didn't say anything...)
'The Sweetest Apu' (DABF14), Apu looks through his records and says "Shankar.....Shankar.....Shankar.....ah! Here we go!" and he pulls out a record named the Concert Against Bangladesh.
In one of the couch scenes, The Simpsons plus many of the townspeople recreate the Sgt Pepper cover.
BABF05 (Take My Wife, Sleaze): The Simpsons go to a 50's diner that has newspapers from the 50's on the walls. One of the larger headlines is "BEATLES FORMED!"
Another one in CABF12 (New Kids On The Blecch): Homer says this "...they're just nonsense words, like 'rama lama ding dong', or give peace a chance."
In 'Treehouse of Horror VI' (1F04): The Devil appears in Flanders-form, and confesses that his deep-down eternally-long secret was to be one of the Beatles.
'Last Tap Dance In Springfield' (BABF15): In the beginning of the episode that Lisa is taught by Little Vicky to become a tap dancer, Homer is at the eye doctors. He looks at glasses and the lady says, "This one is very popular with celebrities, such as Jim Morrison and Yoko Ono." Homer says, "Ewww, she totally ruined the Plastic Ono Band!"
'Bart vs Lisa vs 3rd grade' (DABF20): Principal Skinner had a group of rappers at the school, rapping about the importance of safety, and when they were done the principal said, "Wow, watch out, Beatles!".
'Special Edna' (EABF02): Little Richard is hosting the Teacher of the Year awards. Right when he is about to announce the winner, he says, "I'm a teacher too. I taught Paul McCartney to go OOOOOOOOH!"