Throw It In: "I think it's across the bay, in Alameda." Not written in, but Nichols and Koenig just stayed in character when an extra said it. See here for details.
Leonard Nimoy was trying to crawl out of the water during the final scene, but the rest of the cast members just dragged him back in.
What Could Have Been: Eddie Murphy was originally going to play a conspiracy nut radio personality that filled the story role of the marine biologist Kirk interacts with (minus the romance, obviously). He eventually backed out of the movie but it resulted in a massive change to the storyline. The producers were worried that if Murphy was in the movie it would turn into a guest star movie like Superman III became Richard Pryor's movie. So they made sure the biologist character was clearly a secondary character to Kirk and Spock.