Doubles/copies of the main characters - how often has that been done TOS did it excessively with Kirk, TNG did it too on several occasions. I don´t know that much about DS9 and VOY, but at least they used that theme a lot less in ENT.
There are at least two episodes of Voyager where we get entire double Voyagers with full duplicate crews. This is why Harry Kim and Naomi Wildman in the later episodes are not the originals for "our" ship.
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.