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.
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.