Uhura's Song. Yes, it has a pretty major Mary Sue in it, but I've read that book more than I have any other Star Trek book.
I think that book goes to prove that any trope, even a Mary Sue, can sometimes be done well. Although I think that whether Evan Wilson qualifies as a Mary Sue depends on how you define the term. Strictly speaking, a Mary Sue is a character who is deeply admired by the author and the other characters but has no attributes deserving of admiration by the reader. Evan is a very fascinating and enjoyable character, a delight to read about, so I don't think she fits the definition. She's more of a featured guest star.
I think the rise of the term "Mary Sue" in fan parlance, the notion of a featured guest player as an unwelcome intrusion, has eclipsed the fact that it was fairly common in '60s television to build episodes around featured guest stars, to make them the dramatic focus of an episode with the main cast being in more of a supporting role, or at least a coequal role. The classiest dramas of the era were anthologies, so even continuing series aspired to an anthology flavor. Heck, the show that Roddenberry cited as a model for ST,
Wagon Train, was based so heavily on that trope that most of its episodes were titled "The [Guest Character] Story." And you can see it to an extent in early Trek. The second pilot revolved around guest characters Mitchell and Dehner; "The Corbomite Maneuver" revolved largely around Dave Bailey; "Mudd's Women" revolved around Eve and Harry; "Charlie X" revolved around Charlie; "Balance of Terror" heavily featured the Romulan Commander; etc. I see Evan Wilson's featured role in
Uhura's Song as simply being a continuation of that tradition.