Star Trek is one of the largest media tie-ins around, next to Star Wars novelizations. Although released in multiple series such as The Original Series, The Next Generation, Section 13, etc you can read these books as one large, interconnected story line. This is a reading order for all of the published Star Trek novels done more or less chronologically (there are several time travel novels where it is set in multiple time frames, in those cases it is placed chronologically where the majority of the issue takes place).
I’ve reworked this order. Reading it through, it wasn’t quite right, and really to be enjoyed it should be done with all the media (shows, comics, books, etc). I’ve made a working order that you can not only follow, but create an account and track your reading & viewing. It’s still a work in progress, so if an era you are looking for you don’t see, just be patient. I am adding dozens of listings a day.
If you still only want the books, there is a listing of just books (still in progress also) here: http://startrekreadingorder.com/novel_reading_order.php