“Where No Man Has Gone Before” - I’d like to see a story about the Valiant and how it got out where it ended up leaving only its recorder marker to be found. Hmm, maybe I should try writing that story as a piece of fanfic.
“Balance Of Terror” - A story or stories set during the Earth/Romulan war could be interesting. ENT’s touching on it left a bad taste.
“Shoreleave” - Perhaps we could have seen the TNG crew vist the Shore Leave planet, but then it would have to be a damned good story rather than just treading over familiar ground. TAS had already followed up with its “Once Upon A Planet.”
“The Menagerie” - The real followup here, of course, would be further Pike era adventures. We did get some in a couple of Pocket Books and a brief run in comics with Marvel’s Star Trek: Early Voyages. Now if we ever got an animated series then we’d really have something...
“Space Seed” - We did get a followup: The Wrath Of Khan.
“Arena” - Another Gorn story anyone? Or maybe we could have just seen some Gorns in TNG or DS9. Their appearance in ENT was a huge letdown.
“Errand Of Mercy” - This was followed up by James Blish in his novel Spock Must Die! Of course, for it to be in continuity some way would have to be found for the Klingon’s sentence of exile from starflight to be commuted or appealed.
“The City On The Edge Of Forever” - We did get a followup of a sort with TAS’ “Yesteryear,” but a live-action followup could have been nice but with a sufficiently compelling story of course.
"Metamorphosis” - There was a followup with Judith & Garfield Reeves-Stevens’ novel Federation.
“The Doomsday Machine” - This was followed up by the TNG novel Vendetta.
“Mirror, Mirror” - DS9’s “Crossover” wasn’t a bad followup, but the subsequent Mirror universe stories were evermore disappointing.
“By Any Other Name” - This could have been a good followup with Kelvans returning in search of their advance scouts.
“Jihad” - Although I don’t know how TNG or DS9 could have done it I’d have been intrigued with seeing the Skorr again. However, one can get a sense of how the Skorr could be handled by reading Walter Hunt’s novel The Dark Wing where he introduces a warrior avian species remarkably like the Skorr.
“The Counter-Clock Incident” - In a sense this was followed up with Diane Carey’s novels Final Frontier and Best Destiny.