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).
Tear Jerker: 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.