Looks like I missed a few (timing for the vid link just above)...
5.58 - Him says "I should have known better."
6.00 - Mojo Jojo says "Better run for your live's if you can, little girls."
6.12 - Princess says "You say stop but I say go, go, go."
6.20 - Fuzzy says "I'm going to let you down and leave you flat."
6.25 - Background music sounds a lot like it's parodying "You Really Got a Hold on Me".
6.50 - The background music is the building up in 'A Day in the Life'.
7.09 - As Sargeant Pepper makes his 'Help' speech, the background music is parodying the song 'Sgt. Peppers Lonely Hearts Club Band'.
7.32 - "Who would make a stupid documentry about the Beat Alls anyway." Possibly referring to the Rutles since the reporter is identical to Eric Idle's character...?
7.49. As Prof. Utonium speaks out the words to Yesterday, the same style song plays in the background.
8.26 - During Prof. Utoniums speech the background music parodies "For No One".
8.49 - The last bar of the background music sounds a lot like 'Martha My Dear'.
8.55 - Is the background music parodying "I Want You (She's So Heavy)"?
10.16 - The background music parodies "The Ballad of John and Yoko"
10.43 - A reference to John's "Primal Screaming"?
11.30 - Background music is parodying Ringo's drum solo in 'The End'.
11.49 - Fuzzy says "Cry, babies, Cry."
12.03 - Fuzzy says "See how they fly" - a possible reference to Lady Madonna (See how they run).
12.10 - The Powerpuff Girl says "They're going nowhere, man."
12.17 - The streetsign behind Mojo says "Penny Lane."
12.17 - The building to their left says "Corp."... Possibly a reference to Apple Corp?
12.23 - Imagine on the newspaper is of the half-shadowed Beatles a-la Meet / With the Beatles.
13.30 - "Some day monkey won't play piano song. Play piano song." A phoenetic englishised line from the song Michelle (Son't les mont qui vont tres bient ensemble.)
13.38 - Time for a Beat Alls reunion...
At the end the background music plays the final ever-lasting chord from A Day in the Life.