Star Trek fan fiction stories separate into an overall arc (such as the Mirror Universe or Alternate Timelines), generalized time periods (like In Between Days or Times of the HG Wells), major events (Hold Your Dominion), mysterious genre-crossing events (Interphases), the story of a species or hybridized species (Emergence or Mixing it Up) or even characters as they are followed (Eriecho or Barnstorming).
Several stories and characters shuttle between various arcs. Malcolm Reed, for example,
can be found in In Between Days (Intolerance, etc.), Times of the HG Wells (He Stays a Stranger, etc.), Interphases (Concord), and Emergence (Flight of the Bluebird). Wesley Crusher makes it into Interphases (Crackerjack, etc.) and Barnstorming (Overture, etc.). Gina Nolan steps into Hold Your Dominion and the Mirror Universe.
There will undoubtedly be more crossovers in the future.
Each series can be found under its own page. For stories which can be found in more than one series, they can be found on all applicable pages. Stories are listed in chronological order, and not in the order in which they were written.