My favorites are (in no particular order):
Spock's World by Diane Duane - I adore this book. To me, this is the kind of story that Trek is all about. There was no need for a huge space battle, or a traditional bad guy. It was world-building, intelligent, and well written. Great book.
Ex Machina by Christopger L. Bennett - For all the same reasons that Spock's World was good, so is this. Okay, yes, it had a big space battle, but the point of it was never the battle, but to further explore the characters. One of the best character-development novels of the Trek line, and it takes place in my favorite era, the post-TMP world. I can't wait till Christopher's next DTI novel comes out, I hope we can explore these characters a bit more in it!
The Romulan Way (and, to a lesser extent, the other books in the Rihannsu series) by Diane Duane - I love this book, such a great story, and even today I think of Romulans like this, not as the one-dimensional characters they seem to be in many of the later TV adventures.
Final Frontier and Dreadnought! by Diane Carey - Controversial picks (at least, Dreadnought!), but well written, and just lots of fun. I could read the adventures of George Kirk, Robert April, and Drake every day. They are so well-developed! As for Piper in Dreadnought, well, she may be a Mary Sue, but I was young when I read this the first time, and I loved it. It is just lots of fun!
Ok, I have others, but I'll stop there! Cheers!
Oh, and for Series, you can't go wrong with the DS9 relaunch, especially the first few books!
