Paul McCartney was a Human which along with John Lennon was the answer to the question "Identify the 20th century Earth composers of the following musical progression" in Spock's skill dome environment in Star Trek, at least according to the script. In the finished movie, this reference seems at least inaudible among the many voices in the center, or might have been cut entirely; though not heard on-screen, the line was included in both the novelization and comic adaptation of the film.
The duo was also cited as an inspiration for the Kirk-Spock relationship by Alex Kurtzman and Roberto Orci.
The McCartney-written song "Let it Be" was quoted on the Dedication plaque of the USS Sutherland.
The Paul Rice card from the Alternate Universe series of the Star Trek Customizable Card Game contains an "easter egg" showing the words "daed si luap"; as it spells out "Paul is dead" backwards, this was a tongue-in-cheek reference to the infamous urban legend which claims that McCartney actually died in 1966 and was replaced by a lookalike-soundalike, but numerous "clues" hidden in the Beatles' later works - of which backwards lyrics was one of the most common mediums, actually revealed the truth.