The exchange of the ring parodies The Lord of the Rings movies, with Shrek taking the ring out of the fire (though it is hot in this film, whereas in The Fellowship of the Ring it was still cool) and the inscription on the ring. The shot of Fiona reaching up to catch the ring on her finger is identical to a similar shot towards the end of The Return of the King in which Gollum does the same thing.
Shrek's "I'll kill that cat!" might be a reference to Dinner for One, in which the same line was spoken with almost the exact same intonation.
Puss in Boots bursting out of Shrek's shirt recalls the infamous chestburster scene from Alien.
When leaving for Far Far Away, Donkey sings the theme from Rawhide. Apparently, this was a Throw It In by Eddie Murphy.
After the messenger and his band show up at Shrek's house, one of the trumpet players begins to play the theme from Hawaii Five-O before the messenger stops him.
Shrek refers to the messenger and company as "Sgt. Pompous and the Fancy-Pants Club Band", referring to The Beatles album Sgt. Pepper's Lonely Hearts Club Band.
"K.N.I.G.H.T.S" is a reference to the real-life TV series Cops. Gingy also mentions another show called "Wheel of Torture".
When the Fairy Godmother's factory is flooded with potion, two of the workers are transformed into Lumiere and Cogsworth. A swan is also transformed into a beautiful girl, referencing The Swan Princess.
The swans themselves are probably a reference to The Ugly Duckling and Swan Lake (especially since the swans turn into ballet dancers when they become human).
Puss carves a P into a tree with his sword the same way Zorro carves a Z into his enemies. This also counts as an Actor Allusion, since Antonio Banderas played both characters.