According to this episode, Captain Entenille's name is a reference to the 1970s music duo The Captain and Tennille, comprised of Daryl Dragon (the Captain) and Toni Tennille.
First Mate Cory Scully's name references the show's Associate Producer, 'Corrie B. Scully.'
After spending the night in Zack's room and seeing a ghost, you can see the leg of the crew member under Zack's bed that is taking his blanket.
Zack refers to the Suite Life of Zack and Cody episode The Ghost of Suite 613 when he mentions Irene.