A few more links that I don't think are included in the big list yet:
The Next Generation
Deep Space Nine
- Dark Mirror- References the Lalairu from Rihannsu: Swordhunt.
- Captain's Log: Jellico- Features Honisberg from The Brave and the Bold.
- Star Trek: Unlimited #4- TOS story referenced in SCE: The Future Begins, TNG story a sequel to that.
- Terra Tonight- A sequel to TNG: Full Circle.
- SNW6: The Human Factor- References Q-in-Law
- Devil in the Sky- References the Eeiauoans from TOS: Uhura's Song
- Klingons: Four Thousand Throats- References Excelsior: Forged in Fire
- Millennium Trilogy- Referenced in DTI: Watching the Clock.
- Mosaic- Referenced in The Eternal Tide.
- Marvel Ongoing Comic and Splashdown miniseries- Several issues reference, or are referenced in, the Telepathy War crossover.