Complete Monster: Commander Jefferson Briggs, from Acts of Contrition and Atonement, is an officer with Starfleet Medical assigned to find a cure for the mysterious catom virus. He quickly realizes that he accidentally started the virus when he killed a Borg just as the Caeliar were ascending them to a higher level of existence, causing the catoms transforming it to bond with an airborne virus and mutate it. However, since Briggs sees the Caeliar as a threat to the Federation, he decides to try and control catoms under cover of supposedly searching for a cure. In fact, instead of quarantining the plague and allowing it to burn out, he deliberately spreads it to other Federation worlds, killing thousands. He has already used illegal genetic engineering to create a member of an extinct species whose genome he has been studying and creates 1,961 copies of her, most of which he kills by experimenting on them with catoms. He uses dubious means to co-opt a number of former Borg drones, including children of former drones, as a new source of catoms and, when he learns they feel the pain of the experiment subjects killed by their catoms, is quick to use it as a means of ensuring their cooperation. In the end, the only solution the Federation can come up with is to imprison him somewhere where he'll never be heard of again.
Pretty much all the opening chapters of Homecoming, including Tom's first look at little Miral
''As he watched, she yawned and waved a tiny fist in the air, almost defiantly, as if she dared anyone to come between her and a nap. Tom Paris: She's the most beautiful thing I've ever seen.
Tom's reunion with his dad, who foregoes a lifetime of emotional distance and hugs him.
After Icheb learns about the consequences of the alterations done to him by his parents, how their genetic virus meant to kill the Borg shut off his ability to feel intense emotion (meant to spare him pain during assimilation, and, naturally, not expecting him to ever have the opportunity to experience love), he is still determined to have a romantic relationship with Phinn Bryce.
Iron Woobie: Eden. She blames herself for the death of Admiral Janeway, for whom the crew of her new ship is still in mourning; she is forced to serve under the command of her obnoxious ex-husband; said ex-husband is revealed to be a member of Species 8472 who only married her to make his cover more convincing, and finally, her own Quest for Identity becomes a struggle to stop herself from being possessed by a cosmic force intent on committing genocide and/or destroying the multiverse; all this, while not only keeping a cool head, but doing everything she can to protect the hundreds of lives on her shoulders as commander of the fleet.
The Scrappy: Astall, to a great many (in fact, her species, the Huanni, tend to be this in general to some readers, though they have their fans).
For any dog lovers, there's Janeway's reunion with her Irish setter, Molly, on coming home. After seven years, Janeway's own dog doesn't even recognise her, and Janeway has to sadly admit she's more her ex-fiancée's dog now.
Chakotay's reaction to Janeway's death in Full Circle. Just after they finally decided to become a couple.
What the Doctor does, with Zimmerman's compassionate but misguided assistance, in Protectors. He still loves Seven so much that he cannot endure seeing her with someone else, especially a former womanizer like Cambridge who could easily break her heart, but he also loves her too much to say or do anything to cast a shadow on her happiness. His only option is to use technology to suppress his feelings ... and it still doesn't completely work.