Vampire Hunter Victoria Calandra of Charby the Vampirate is an incredibly kind girl if a bit of a Workaholic that started hunting to save lives and doesn't consider herself to have any time for fun or romance due to the incredible responsibility of her work.
This is deconstructed with his Dumbing of Agevariant, on the other hand, as his unnerving and unfailing devotion to his girlfriends ends up being a major turnoff.
Tom of El Goonish Shive is the fake, manipulative version—in fact, he's too malicious to even count as a Dogged Nice Guy, he's just a straight-up Manipulative Bastard. Good Tom, however, is a parody due to being a perfect, genuine Nice Guy. He apologizes for getting offended for overhearing "Tom is a jackass" (they were talking about the other one), is appalled at the casual misogyny of a romantic comedy, and genuinely apologizes to his girlfriend for taking her there on a date, even though she doesn't care. Oh, and he may or may not have a superpower that lets him tell when random heroics are needed.
Good Tom: WAIT. A puppy is in danger. Tom's Girlfriend: Again? Good Tom:Quickly! We must make haste! [runs off] Tom's Girlfriend:[following] You are the worst best boyfriend ever!
John Egbert is definitely one of these. General consensus among his friends is that he's kind of a doofus, but that there's something endearing about his derpiness.
Jade meanwhile is a Cloudcuckoolander who tends to have mysterious premonitions, but is largely a kind, polite, upbeat girl. She is initially upset by the trolls' antagonistic behavior, but is quick to forgive once Karkat extends an apology.
Kanaya Maryam (aka grimAuxiliatrix) of the trolls is considered by many to be a Nice Girl. Polite, well-spoken and helpful; although she's a meddlesome meddler, she apparently does it only to help people. "Auxiliatrix" even means "a helpful woman". It remains to be seen if she has any ulterior motives, however.
Tavros Nitram also qualifies. One of the trolls notes that he seems to be unable to hate anyone. Which is really odd among trolls.
The pre-Scratch trolls bring us Tavros's dancestor Rufioh, who's just too nice for his own good; Kanaya's dancestor Porrim, the Ethical SlutTeam Mom; and, oddly enough, Vriska's dancestor, Aranea, who is almost faultlessly polite and forgiving, and whose main negative trait is that she likes to talk a bit too much. At first glance. Underneath everything and when it comes to making plans she turns out to be about just as bad, if not worse, than Vriska.
Sedgewick from Lackadaisy, whose only faults are his constant need to overwork, being too polite, and once killing a duck that still haunts him to this day. And with the reveal that one major character is about to die, some of the fandom has decided it has to him, because he's just too likable.
Mokepon's Kahn Miles is probably the nicest Nice Guy you'll ever meet. He treats Atticus with respect and kindness despite all the crap he gets from him, including saving his life, and he let Atticus beat his already wounded pokemon because he knew it would make Atticus happy.
Stand Still, Stay Silent: Among the group of Norwegian friends in the prologue, Aksel. He spends the segment trying to arrange for his grandmother to come stay with him during the worst of the Rash, while his three friends are either having a Cosy Catastrophe attitude towards an ongoing storm, complaining about getting the previous day's newspaper despite the fact that they were only interested in the crossword puzzle or generally being The Gadfly.
Touhou often depicts Reimu Hakurei as an example of Good Is Not Nice, but in the fan comic Touhou Journal, Reimu is depicted as a Cute Mute with unconditional kindness, doing favors such as reading bedtime stories for Remilia (don't ask how she's able to do it), befriending a lonely Nue, and cheering up Marisa when she leaves a party in a troubled mood. When Aya, accompanied by Momiji, tries to sneak up on Reimu in an attempt to catch a scoop on Reimu having a darker, less-than-kind side, not only does Aya fail, but when Reimu spots them, her response is to cheerfully serve them tea!