Donkey's "That's a nice boulder"◊ is a reference to Sylvester and the Magic Pebble by the same author as Shrek. The "boulder" was a donkey who turned himself into one to escape from danger but couldn't turn back when he couldn't reach the pebble. Fortunately his parents found him and wished him back.
Robin Hood and his musicians could be from any whimsical version of the story, but most likely Robin Hood: Men in Tights. Fiona's subsequent thrashing of them is likely an homage to Crouching Tiger, Hidden Dragon but blatantly parodies The Matrix (that sequence in particular may have been added basically at the last minute, something that would have been impossible with hand-drawn animation).
When Donkey manages to make it to the other side of the bridge through some panicking, Shrek pats his head and says, "That'll do, Donkey. That'll do." This is a reference to the final line of Babe - "That'll do, pig. That'll do."
When looking at the constellations, Shrek points out Bloodnok the Flatulent, a reference to Major Bloodnok from The Goon Show.
The Kingdom of Duloc is a big reference/Take That! at Disneyland, with the dolls signing "Welcome to Duloc" being a pastiche of "it's a small world". In fact, the song has a segment with identical rhythm (the melody is different) to the verse of the aforementioned.
When Farquaad asks the Mirror for a girl to marry, he offers three bachelorettes in the style of The Dating Game.
Donkey's line, "You might have seen a housefly, maybe even a Super Fly, but you ain't never seen a donkey fly" is likely a reference to the song "When I see an elephant fly" from Dumbo, which made similar puns.
Right before that, a reference to Disney's Peter Pan:
Peter Pan: He can fly! 3 Pigs: He can fly! Head Guard: He can talk!
Fiona’s “transformation” copies the Beast’s transformation from Beauty and the Beast.
The Mother Goose's attack on San Ricardo is very similar to Godzilla (1998), right down to the final assault on the bridge (and her attacking Humpty's plane from below, just how 'Zilla chomped a helicopter in the movie).
"His boots are made of soft Corinthian Leather" is a reference to Ricardo Montalbán (one of the most prominent Hispanic actors in early Hollywood) and his famously suave endorsements for Chrysler. Montalban also co-starred with Banderas in Spy Kids 3-D: Game Over, and it's very likely "San Ricardo" is named in his honor. The use of the reference in relation to Puss' boots is also a Call-Forward to a similar reference in Shrek 2, where Donkey says to Puss "Hey man, you wanna get your fine Corinthian footwear and your cat cheeks out of my face?"
Jack and Jill's little ones are ten little piggies.
Humpty at one point tightens his golden suit so that only his eyes are showing, and starts mumbling in an incomprehensible way. Kenny, anyone?
◊ is a reference to Sylvester and the Magic Pebble
