I have a few.
-One person on the crew feels like an outsider or is deemed somehow as "different" (Spock, Data, Odo, EMH, T'Pol) and the theme appears throughout the show repeatedly.
-Person fakes their identity to try and deceive the crew of a ship. Ship's captain or a crewmember finds out.
-Crewmember or Captain becomes possessed by another entity of some unknown species.
-Captain refuses to go to sickbay even though it's necessary.
-Captain or crewmember bends or breaks the Prime Directive in order to do good.
-There is a debate over whether something/someone is actually a sentient being with rights.