"Series" by era, ship, Captain
I try to stay focused on the "framing" or "present" sequences, even if a story is primarily set in another time-and-place.
I probably misplaced a bunch, since I haven't checked every one, and don't have access to some DC and IDW comics in case MA and MB info is sketchy.
Additionally, some items in the "2260s" (most five-year mission stories) and "2280s" (most movie-era stories) eras may in fact occur in the early years of the next decade but are placed there due to lack of specific dating information (or my lack of knowing it).
And this is most assuredly not a timeline, merely a lumping of stories set on the same starship, in the same decade, under the same Captain (or main character).