Thinking of Last Week's Tomorrow and Tomorrow and Tomorrow and how they shifted things around for new canon in regards to Khan.

Strangers from the Sky, I have a dim memory of having read as a kid, with Earth's first unofficial contact with Vulcans in 2045.

Federation, released a year before Star Trek: First Contact covers WWIII, TOS and TNG eras as we follow a quest for revenge against Cochrane.

Starfleet: Year One had a series of chapters in novels published in the late 90s and collated into one novel....released in 2002. Had a disclaimer that it did not relate to Enterprise.

The Eugenics Wars vol 1&2 some of my favourite rewrites of history, weaving Khan into modern day fabric and shows how the wars were fought in secret.

There's also

A TNG Mirror Universe novel from 1994 that got demolished by the first DS9 Mirror episode ("Crossover") that aired that same year!

Also, Also

TOS The Mirror Universe Saga is an alternative Star Trek IV

Ah yes, a favourite of mine as a kid. As I found later, not so much an alternate tho, as in “this is what happened between Trek III and IV, and then when they found out how Trek IV went down, wrote a giant undos, including Spock losing his ship he earned here, Kirk stealing a ship again to take Spock back to Vulcan as the mind meld initiated by Mirror Spock deteriorated, basically placing them all back where they needed to be, ready for Trek IV. A Secret History.

Really DC’s First Run is its own internal consistent thing tho. It also gave us Konom, the First Klingon in Starfleet (years before Worf), and Ensign Bearclaw with a Kirk-sized chip on his shoulder (honestly I could take or leave the latter) culminating in the Who Killed Captain Kirk story (also re-released in graphic novel format).

Then when Trek V happened they decided to do a Hard Reset on the comics and start fresh and goodbye to all that internal history, and hello R.J. Blaise, and Sweeney (Not Sweeney!), Ensign Fouton and Not-M'Ress and a Starfleet Admiral or Commodore who was a Klingon plant….and then we chucked all of that after a dozen issues or so to do more episodic arcs instead with almost no mention of those new characters (tho we did resolve that Commodore storyline incidentally and revisited R.J. years later in a one-off special…)

Oh this reminded me, another piece that canon settled in the 90s, Kor, Kang Koloth showing up in modern makeup in DS9. Kinda undoing another of my favourite graphic novels:

Debt of Honor, which weaves an extragalactic threat trough Kirk’s service as a lieutenant on Farragut, through the five-year mission, post-TMP and finally post-Trek IV, along with an older, smooth Kor. (T'Cel, a Romulan spy turned Commander, is also great) and the coda of Cry Vengeance culminates in a battle between Jamie Finney (Ben Finney’s daughter from "Court Martial”) challenging Gowron to fight with Bat'leths, Kor long dead…..