To be fair, the X-Men crossovers make it pretty clear that Earth-616 (comicspeak for the main Marvel Universe) is separate from the universe in which Star Trek occurs.
Well, the original TOS/X-Men crossover did so. The TNG/X-Men comic didn't quite follow suit; there was a portion where one of the TNG characters referenced something from Marvel history as though it were part of Trek history.
As for SNW stories with novel-continuity ties, here's what I'm aware of:
SNWIII: TOS: "The Aliens are Coming!" by Dayton Ward: Referenced in The Eugenics Wars
SNWVII: TNG: "Full Circle" by Scott Pearson: Draws on elements of novel continuity.
SNW09: TNG: "Terra Tonight" by Pearson: Sequel to the above.
SNW09: DS9: "Shattered Allies" by Emily P. Bloch: Draws on concepts from DS9 Relaunch, but isn't completely consistent with it.
SNW09: Speculations: "The Immortality Blues" by Marc Carlson: Built around the events of WWIII as depicted in The Lost Era: The Sundered