You've got to be kidding.
It would take me at least 24 hours to find and list them all. That would be highly illogical.
The above is correct. A comprehensive list would be a tall order.
A synopsis, on the other hand, is reasonable. I'm assuming this question refers to Original Series references in latter spin-offs or incarnations of Star Trek.
I invite future respondents to add examples to the following lists. Here goes...
Examples From TAS Edit
The Animated Series has the same cast as The Original Series and is replete with references. Knowledgeable people are invited to list examples, here.
Examples From Movies 1-6 Edit
Khan in Wrath of Khan is a returning villain from The Original Series. Ricardo Montalban played him both times.
In Star Trek 3, the Vulcan male sexual issue called Pon Farr is used as a plot complication. It was first referred to in TOS.
Examples From TNG Edit
Despite the considerable, chronological gap between TOS and The Next Generation, three principle characters managed to appear, not abetted by time travel:
- McCoy apparently took sufficiently good care of himself that he managed to stay alive long enough to see the Enterprise D off in the pilot episode.
- By a similar token, Spock could rely on his natural, half-Vulcan longevity to ride out the years. His self-initiated, diplomatic work on Romulus attracted a visit from the Enterprise D. After those events played out, Picard consented to a telepathic sharing of Spock's father's appearance aboard Enterprise D.
- Scotty once beamed out after programming a transporter not to beam him back in until rescuers arrived.
Picard once mentions Khan in the same breath with Hitler in the Matter of Time episode.
Kirk's final appearance, to date, was in Star Trek: Generations. (That's Kirk Prime.)
Examples From DS9 Edit
Dr. Bashir remembers a historical account of Kirk discovering what we fans call "the Mirror Universe" in the first of five episodes revisiting that reality.
In Trials & Tribble-ations, many crew-members travel back in time to the Original Series Trouble With Tribbles episode and interact with the original crew. Toward the end, Sisko gratuitously introduces himself to Kirk.
Examples From Voyager Edit
In the ret-con story of Flashback, we learn that Tuvok served under Captain Sulu. Thanks to melding with Tuvok's infected mind, Captain Janeway gets the privilege of seeming to interact with Sulu. This was (correct me if I'm wrong, Trekkers) the last time a TOS character appeared on a television episode.
Since the holographic Doctor program had constant access to every medical database and physician personality file on record, he co-opted McCoy's catch phrase more often than any other Doctor, even breaking old Bones' record for number of variations used.
Examples From Enterprise Edit
Enterprise is a retroactive continuity series set before TOS. Therefore, it could not logically contain references of the type called for by this question. There are, however, time travel story arcs which defy logic to the extent that time travel premises must.
In one case, Captain Archer is perusing a future library and discovers some text reading "Romulan Star Empire," cluing him into its existence. (Just this once, I'm going to skip looking up the episode name.)
New Star Trek (2009) Edit
The eleventh Star Trek movie (simply titled Star Trek) essentially is a 127-minute-long reference to TOS. All new actors play youthful versions of the classic characters facing an alternate debut situation brought about by time travelers from their future.
One of the time travelers is TOS character Spock, still played by Leonard Nimoy, at the oldest age he's been depicted yet. (To distinguish this Spock from his young counterpart, he's scripted and billed as Spock Prime.) Spock alludes to his decades-long friendship with Kirk which began in TOS.
This makes Spock Prime (correct me if I'm wrong on any count) the oldest principle Star Trek character, the character whose personal story spans the longest time, and the only Star Trek bookend character. (That is; he's the only character to appear in the oldest and newest incarnation of Star Trek.)