My long-time (meaning like, a year or two) favorite "sleeper" is Web of the Romulans, despite the amorous computer subplot. I thought it had a nice mini-epic quality to it.
Newly challenging it for the position, though, is The Vulcan Academy Murders. In truth, I found the A-plot to be lacking, and I guessed who the murderer was pretty much the moment that character was introduced, just based on genre cliche. But what the big did do well was give a very interesting, in-depth look at certain elements of Vulcan culture. Since I haven't yet read Spock's World or the Vulcan's Noun books, this is pretty much my first really exposure to that type of thing, and I quite enjoyed it.