* FanWank: Like a lot of expanded universe stories, the novels often go to great lengths to explain away continuity errors from across the various ''Trek'' series. Taken to extremes in ''Tower of Babel'', which attempts to weld together all the many disparate references across over 40 years of canon to planets called Rigel and aliens called Rigellians into one huge star system with numerous planets and moons inhabited by dozens of indigenous and migrant life forms, even going to far as to include background creatures from ''Film/StarTrekTheMotionPicture'' only named in production materials.
* SugarWiki/FunnyMoments:
** ''Uncertain Logic'' begins with a Vulcan medical student being taken hostage by a panicky Malurian. Being a Vulcan, she just snarks though the whole thing, and when she defuses the situation is annoyed because it's interrupting her work.
** Archer having an awkward encounter with a very pregnant T'Rama, who shows the sarcastic chops her grandson will use to deadly effect.
** Even Soval is ragging Archer about that gazelle speech. Hell, Vulcans who've never ''met'' Archer know about the gazelle speech.
** Having been captured again, T'Pol remarks how often it is that when she's around Archer she ends up "in bondage". There's a very long pause before Archer just says he's not going to say anything about that.
* HarsherInHindsight: ''Live by the Code'' has Section 31 using hideously unethical means to get rid of the Ware just so the Klingons would back off from attacking the Federation. As ''Discovery'' shows, as horrific as the consequences are, Section 31's actions probably saved the Federation from a fight they couldn't win.
* SugarWiki/MomentOfAwesome:
** Val Williams, looking for Kirk and Gev, sees a member of the First Families about to rape a ''very'' young girl (he likes 'em young). She tries to tell herself she can't get involved... then she hears the clothes ripping. Cut to afterwards, Val's fleeing with the young girl, having beaten some shades out of the guy.
** Later on, Val managing to talk Garos into realizing the First Families are going to betray him. And he agrees, saving her via transporter. For added bonus, Garos reveals he'd been collecting blackmail on the families, just in case... which he unleashes.
** During ''Uncertain Logic'', as anti-alien sentiment starts rising across Vulcan, Phlox, Iloja and Tobin go to a cafe. Phlox is nervous given his experiences on Earth after the Xindi attack. As the debate gets heated, several Vulcans opposed to the V'Las supporters get up and stand [[GoThroughMe in front of them]].
** Tobin Dax manages to be a monkey-wrench for V'Las's plans twice over - first, his knowledge of magic tricks allows him to help Skon work out how the ''Kir'Shara'' was taken, and later on his engineering expertise and good memory allow him to work out how to save the ''Endeavor'' from sabotage, proving you don't need to be a badass to be a badass.
* MoralEventHorizon:
** [[spoiler:Section 31 deciding to let Maltuvis take over Sauria in the name of realpolitik.]]
** [[spoiler:Later on, their using the anti-Ware code to annihilate the tech, dooming dozens of civilizations that need the tech just to have civilization.]]
* TearJerker: The death of the ''Vol'Rala'' crew at the end of ''Live by the Code''.
* TheWoobie: Malcolm Reed, who finds out in ''A Choice of Futures'' that [[spoiler: he may never be able to have children because of accumulated damage from his years of using the transporter.]] He also admits to having a lot of trouble making new friends and is clearly rather upset about the splitting up of the old team as everyone gets promoted and moves on to other ships.