I'm pretty sure that Donkey Hotay is a play off of the novel Dontay Hotay. (sorry about spelling)
One only witchdoctors will get: Kan Po has a line in Beachhead, "Welcome my Captain ... to the Machine!" sounds kind of like the Pink Floyd song, "The Machine"
Old Bird Hekins (chicken miner) has a line, "I'd have gotten away with it, too, if it weren't for you blasted pirates." which is sort of like the trademark line from the Scooby Doo cartoons.
Gilbert has a line in the quest With Catlike Tread, "to sit in solemn silence on a dull dark dock in a pestilential prison with a lifelong lock." I'm not sure what this is a reference to, but its a common tongue twister in theatre.
I believe I posted this somewhere else, but there is a quest in the Gold Mine called Barrels of Monquistans, which may be a reference to the barrels of monkeys toy.
Floatsam is a name for debris of ships that are floating in water.
Arroyo Grande is a play off the Grand Canyon (an arroyo is a dried riverbed)
The Free Ranger in Cool Ranch is a play off of the Lone Ranger (character from old radio shows and 2013 Johnny Depp movie)
There is a Musketeer Ability called True Grit, and True Grit is an old western movie and a novel, by Charles Portis
The whole Jack storyline reminds me of Dr. Who. After all, the Prawns have been stranded by an ancient war, and the Master is their ... master? (I confess I don't really know that much about Dr. Who)
Manny's first quest, The Pirate That Time Forgot is a reference to the movie The Land That Time Forgot (which was about an island where there were dinosaurs)
There is a quest called Message in a Bottle, which is probably a reference to the Police song.
The quest in Beachhead is called the Guns of Marleybone, which is a reference to the "Guns of Brixton" song by the Clash.
Wow ... there certainly are a lot of references.
Ivette Xavier, Oracle
It makes me oddly happy to know that I'm not the only one who got the Pink Floyd reference.