The Best of Trek #3 features "Alternate Universes in Star Trek", a guide to the little non-Trek references in James Blish's Trek adaptations and novels. If you use any of this stuff, credit belongs to Mark Andrew Golding (hope he doesn't mind!).
From Blish's adaptations:
"City on the Edge of Forever" references Bonnar the Stochastic from
The Triumph of Time.
"Tommorow is Yesterday" mentions the Vegan Tyranny from his
Cities in Flight series.
"Miri" references the Cold Peace, also from
Cities in Flight.
Spock Must Die! references the Xixobrax Jewel Worm from Blish's short story "This Earth of Hours", part of
Galactic Cluster
And one from me...
Spock Must Die! also references James' short story "Dirac" (or was it called "Beep"?)
The article claims that James Blish saw Star Trek as part of a multiverse, where his other books and stories existed in parallel. The dates of events changed, but the same aliens exist across the universes and events are similar.