In the past I have talked up the first two Myriad Universes books, which each contain 3 "What if?" stories, each of length about half a normal Trek novel. A third, Shattered Light, came out in December, and I've finally got around to reading it. The three stories and branching points from regular Trek are:
The Embrace of Cold Architects - The Borg arrive slightly sooner than in Best of Both Worlds, which has two major consequences: things play out differently with Data's daughter Lal and she doesn't last a single episode length, and when the Enterprise fires on the Borg ship (like the season 3 cliffhanger)... the attack succeeds.
The Tears of Eridanus - In Star Trek as we know it, the Federation is very Earthy. The capital city is on Earth, Starfleet comes from the Earth Starfleet's traditions, and beings with two arms and two legs are called humanoids. This story takes place in a world where Andor is the center of an Interstellar Union (including Earth), where people (mostly andorianoids) serve in the Interstellar Guard. The reason for this difference isn't clear at first and some will pick up on it sooner than others, so I'll leave that unsaid. This specific story then involves Sulu as commander of a vessel on a rescue mission.
Honor in the Night - In "The Trouble with Tribbles", Arne Darvin is exposed as a Klingon undercover agent. What if a shuttle accident meant the tribbles weren't around to help force this reveal? This story covers a few key players in a new history of Klingon-Federation relations from that point to TNG times.
I found the first story a bit meandering, but the other two present some pretty interesting alternate worlds.