There are hundreds of Star Trek novels out there, very few people are able to read all of them. These are the few that I recommend from personal use. Your mileage may vary. Star Trek Novels, DVDs, and Videos available from Amazon.com. You can also find some more of my personal recommendations here.
Peter David
It is an almost automatic purchase for me when I see Peter David's name as the author of a Star Trek novel. His grasp of the characters and the world is simply wonderful and usually a little offbeat. He doesn't write enough of these anymore.
Peter David, K.W. Jeter / Mass Market Paperback / Published 1993
The New Frontier
These are not the usual run of Star Trek books. They are set in the same time frame as the Next Generation and Deep Space 9 but only a few of the characters are from the series. They explore a different part of space, with different races, and very different politics. Lots of fun, for as long as Paramount lets Peter get away with it.
Josepha Sherman, Susan Shwartz / Hardcover / Published 1999
The sequel to Vulcan's Forge, we meet a lot of old friends, including some very unexpected ones. Plus there is the Vulcan wedding and the Romulan revolution. Well worth picking up.
Dean Wesley Smith / Trade Paperback / Published 1998
An anthology of Star Trek short stories, most of them fan written from a contest put on by Pocket Books. Ranging from the original series to Voyager, there is a large mix of styles and types.
A look into the Star Trek phenomenon from a worldwide perspective. Greenwald talks to people from Leonard Nimoy to Patrick Steward to the Dalai Lama about Star Trek and how it has affected the world. He travels from England to India to Hungary to Japan talking to ST fans. Clear writing and a very diverse collection of information make for a fascinating read. I don't know that I agree with Greenwald's assessment of Roddenberry being a genius, but his creation has certainly touched the world.
This is Walter Koenig's autobiography. The cover is great and the inside is a really good read. If you are a fan of Walter's work, whether Star Trek or Babylon 5, you should pick this up and read it. It makes me want to meet the man and get to know him and not because he is a TV star.