(written from a Production point of view)
In-jokes are comedy elements added to a production or a situation. The comedy comes from shared knowledge between a specific group such as co-workers, members of the same organization or people with a shared belief or knowledge of a shared situation.
There are many in-jokes that people have added to displays and scripts for Star Trek over the last 50 years.
- the recurrence of the number 47
- various displays on okudagrams and indeed the name okudagram itself
- references in the Star Trek universe to other science fiction shows and movies
- the "sharing" of planets and species between Star Trek and other science fiction
- nicknames for production staff or crew making it into references within continuity (see: great bird of the galaxy) and so on.