As a rule, Star Trek makes no effort to maintain continuity outside of its Live Action Television series and films -- in fact, for a while, there was a directive that tie-ins couldn't reference anything except the live-action canon. Novels, comics, video games, roleplaying games, technical manuals etc. draw from their common origins, but exist largely independent of each other save for occasional Shout Outs or borrowed elements.
There is a modern line of Star Trek novels from Pocket Books which make an effort to be consistent in regards to continuity. Most novels from the year 2000 on are generally set within the same reality. This continuity is discussed on the Star Trek Novel Verse page.
Some of the older books have been retroactively absorbed into the "Novel Verse" continuity, most have not.
There are (naturally) many Star Trek comic books, including:
- Star Trek Starfleet Academy (Marvel series, 1996-1998)
- Star Trek Deep Space Nine: N-Vector (Wildstorm miniseries, 2000)
- Star Trek The Next Generation: The Gorn Crisis (Wildstorm hardcover, 2000)
- Star Trek Divided We Fall (Wildstorm miniseries, 2001)
- Star Trek Countdown (IDW miniseries, 2009: Billed as the "official prequel" to Star Trek and written by the screenwriters, it initially wasn't clear whether this is merely a part of the Expanded Universe, or canon in its own right. After being questioned on certain (minor) inconsistencies between the comic and the final version of the movie, the screenwriters declared it non-Canon.
- Star Trek (IDW series 2010-date: A retelling of Original Series episodes based on the alternate timeline started off by the 2009 film.)
- Star Trek: The Next Generation/Doctor Who: Assimilation² (IDW miniseries, 2012): Crossover miniseries with Doctor Who