The sound effects used for both of the trajectory computers for the Bebop and Doohan's ship are sections of the boot-up sequence of the computer, MOTHER, from Alien (1979).
In Session 19: Wild Horses, the man who owned and fixes Swordfish II, Spike's spaceship, is named Doohan. This is a reference to James Doohan, who played "Scotty" on the original Star Trek (1966) TV series.
In this episode, the crew is hunting a trio of pirates named George, Harman, and Ruth. George Herman Ruth is the real name of Babe Ruth, the legendary baseball player who started his MBL career as a pitcher for the Boston Red Sox. Also in this episode, a mechanic named Miles is a die hard fan of a fictional baseball club Blue Sox.