Donut on the Red Team is so perky, friendly, and sweet that even Church (who otherwise hates everyone) likes him. He's essentially the closest thing RvB has to The Cutie.
Caboose seems to be vaguely aware that half the people he knows are supposed to be his enemies, but that doesn't mean they can't be his friends.
Sheila is remarkably personable and helpful for literally being a tank, and is a Cute Machine.
The Freelancers have their own sort of Power Trio of Nice Guys in the form of Agents New York, North Dakota, and Washington. York is incredibly snarky, but has a strong sense of fair play and right and wrong and his snark is usually intended as good-natured. Wash is the dorkiest one, worried about following the rules and everyone getting along. Lastly, North is the Team Mom, so nurturing and caring that he was specifically given the most child-like of the AIs as a result.
Ruby Rose counts as well. She carried Jaune Arc to initiation when he got pinned to the wall by Pyrrha at Weiss's behest. She accepted Penny as a friend after Weiss bumped into her, despite protest from the other girls. Also, even though Weiss antagonized her throughout Volume 1, Ruby still expressed concern for her teammate after learning of her troubled childhood.
Quite a few characters in Survival of the Fittest, but one character who plays this to a tee is Reika Ishida, in contrast to her sister. One of her defining traits was that she was nice and friendly, always trying to help out. However, true to the stereotype, she literally gets killed within two posts once she gets to the island. Danya in the following announcement then called her "the less interesting of the Ishida sisters" for this reason.
Doug Walker's niceness was lampshaded and parodied in his cameo for Phelous's review of House of Wax (2005). While the rest of the site cheered for Paris Hilton's character's death, he's disgusted by their behaviour even though she's fictional.
Speaking of TGWTG, the late and much-missed JewWario (even in character, which was close to his real life persona anyway) was probably THE nicest person out of the entire cast/crew.
Rack of the Whateley Universe. He's a dwarf on top of being a mutant, but he has several extremely pretty female friends because he treats them well. And he makes the time to explain to Chaka why she should watch out for the dreaded Sahar.
In Worm, the superhero Legend, leader of the Protectorate, inspires an almost universal "he's so nice!" reaction in people who meet him, and is generally considered the nicest member of the Triumvirate, with Alexandria being cold and distant and nobody liking Eidolon. As it turns out, he's also the only member of the Triumvirate that isn't aware of the horrible crimes perpetrated by Cauldron.
There's also a twisted inversion of this trope in the form of a villain actually named "Nice Guy." He pretty much renders everyone around him incapable of regarding him as a threat, and most people actually trust him and think of him as a friend, allowing him to calmly walk up to people and start murdering them where they stand, with their friends blithely standing by and unable to do anything about it because he's such a nice guy.
Grace Poole is a Composite Character, combining mild and kind Mrs Fairfax and scary, mysterious Grace Poole from the book. She's very intense and weird during her first appearance. Later she has moments when she's genuinely nice to Jane and very caring. Other times she seems nervous, impatient or downright nasty.
Jane expected Mr Rochester, her employer, to be horrible, based on Grace's vague description and Adele's nightmarish drawings of him. She finds out he's not abusive, which she thought he would be, but he's teasing, weird and bossy. In episode 13, Jane says that he seems a nice enough man, though a little negative, moody, sharp, dismissive,... but in a good way. There are obviously things which haunt him.
Deckard in Bee and Puppycat makes Bee a casserole after hearing she lost her job. He even leaves it for Bee after she accidentally Groin Attacks him with her umbrella.