In Survival of the Fittest, Dorian, one of the terrorists behind the Act, has been shown to send most of the money he earns from working in the organisation behind SOTF to his mother. It helps that he's well... pathetic too.
In Suburban Knights, after spending the event tricking and manipulating the reviewers of his site, all while he himself refuses to play along and act in character and generally is a selfish bastard, the Critic is genuinely worried about Team 2 after he figures out that the map he got in a chain letter was sent by Malachite, and that Team 2 had no way of knowing that there was an Evil Luddite tracking them down. Immediately after, he and the rest of Team 1 band together to take down the next obstacle, so that they can quickly find Team 2 and warn them. (Given how the reviewers in general had their turns as jerks, this would count for them all in general)
Likewise despite everyone despising Mati and constantly sending him off on Snipe Hunt s to keep him out of their way, once he suddenly shows up while Malachite (a dark wizard who was beating all up them up rather badly) is there and starts yelling at him because he's frustrated with everyone else they all show serious concern for his well being and try to warn him to leave, instead of simply allowing Malachite to kill him without protest (which would get him out of their hair forever)
The Cat in the Hat shows the only two things The Nostalgia Critic cares about enough to stand up for: children and Dr. Seuss.
In There Will Be Brawl, Wario, the series' resident sneaky and manipulative bastard, is revealed to also be taking care of his mentally-handicapped brother, Waluigi.
Then blows all the acquired sympathy by using him to deliver a bomb to Red.
There's also a subversion when he apologizes to Red's girlfriend for causing Red's death, offering her money to make amends. As he walks towards her, the audience can see him holding a Home Run bat behind his back. Fortunately, Leaf is not fooled and kills him with Jigglypuff.
The Emperor of If the Emperor Had a Text-to-Speech Device shows a few times that he's actually a Jerk with a Heart of Gold: he admires people who are willing to sacrifice themselves meaningfully, such as Ollanius Pius and the Astral Knights, and gives Magnus a really cool war motorcyclenote Which the Imperium doesn't make anymore and forgives him upon the two's reunion.
Subverted in episode 18.5 when he calls his son "special" (in a good way), only to add that he's still part of a failed batch. Suffice to say, Magnus is not amused.
Horus of all people gets a straight example in the same episode - when Malal has a mental breakdown over himself being uncanonical, he consoles him and offers to make him hot chocolate.
The Emperor also has a surprisingly touching moment with Ecclesiarch Decius. He initially considers Decius just another symptom of everything he finds wrong with the modern-day Imperium and is not shy about saying so, but ultimately realizes that while Decius is severely misguided, he is a genuinely good man who is doing his best for humanity. It's this realization that ultimately leads to the Emperor deciding to massively reorganize and reform the Ecclesiarchy, rather than outright disbanding it as he had originally intended.
Despite all her abuse, The Nostalgia Chick's shown affection towards Nella on occasion. The end of her Ever After and My Little Pony reviews give the impression that she knows how ridiculously adorable Nella can be and loves it like the rest of us.
From the Global Guardians PBEM Universe, Diabolical Mastermind Lord Doom was one of the primary researchers behind the AIDS cure. He provided the cure to the world not for any underhanded ulterior motive, but because the AIDS epidemic was killing innocent people and he wouldn't stand for that. He also gives tens of millions of dollars to charities every year.
The entire SCP Foundation adores SCP-085, an animated drawing of a young woman named Cassy who has become aware of her medium and fallen into depression as a result. Considering most of the SCPF's actions toward sapient SCPs are... professionally detached, it's cute to learn that one of the first requests they had for a magical vending machine was "something Cassy will like" (it produced a cup with an illustrated milkshake on it, which Cassy said was "delicious").
"SCP-076-2 has however, shown that it has great knowledge of human anatomy (although in a highly violent context), military tactics of open warfare, metallurgy, and, strangely enough, the care of livestock."
In Shadowhunter Peril, Oblivion the single most powerful being in the entire story, and who can turn into something that resembles a near-Eldritch Abomination-type creature, enjoys murdering helpless civilians for fun, then stabs the entire resistance in the back by a attempting to kill Puriel and joins the enemy because he was bored of not being able to fight anybody. Word of God states that he has an unwaveringly fierce love for kittens.
Kenji, a paranoid misogynist conspiracy theorist, makes unsavory remarks about the girls, steals books from the library and borrows money without paying it back. However, on Lilly's route, when he accidentally runs into her, he offers to help her up, and when Hisao finds out that Lilly is leaving for Scotland, he offers to talk with him if he needs it. In Shizune's route, after Hisao gets a "Dear John" Letter from Iwanako, he fondly talks about his old girlfriend.
Shizune, as Student Council President, has a reputation around Yamaku as incredibly bossy, and as a result, everyone besides her best friend and interpreter, Misha, left the council. However, in Hanako's route, she helps Hisao take Hanako to the nurse's office when she suffers a panic attack, and it's implied that she likes and is concerned about Hanako, but can't get close to her because Hanako's best friend is Lilly, who is in a feud with Shizune. In Lilly's route, Shizune manages to reconcile with Lilly. In Shizune's own route, she reveals that all of her actions, starting with her attempts to recruit Hisao to the student council, were done so that he would snap out of his depression. She also states that making people happy and engaged is her goal, and she hopes to become a philanthropist.
YouTuberRepoNut, a repo man who posts videos of his repossessions, brings his dog on some repos and literally pets her at times.
Ultra Fast Pony. In "The Penny and Clyde Show", Discord confronts Fluttershy, alone in the maze. Flutters is terrified, and asks to just be left alone... and Discord immediately obliges.
David Chapman of you could make a life is an angry, bitter young man with No Social Skills who focuses on hockey to such an extent that he alienates everyone who tries to get close to him. But when he learns that a member of a rival team suffered a Career-Ending Injury, he sends a genuinely concerned text message asking about him to Jake, the captain of that team. He also apologizes for being a dick when he learns that his biased assumptions about Jake were completely wrong.
A Giant Sucking Sound: President Ross Perot asks like a raving Jerkass many times, but that doesn't stop him from putting an end to the Rwandan genocide, sending aid to Japan after Nagoya is nuked, and standing up to China over Taiwan's sovereignty.
The murderer from Doors isn't above kidnapping the narrator's sister and killing his parent's but the most he does to the dog is pet him and say "good boy."
In the 2014 D 20 Live campaign, after wiping out the whole party, Big Mike decides to ignore Linkara's command that Fussy Britches (a four-armed gargoyle polymorphed into a kitten, tamed by the party, and then gender-swapped and alignment-switched into a Chaotic Good female kitten) poops on Acererak's skull and has her use her prior knowledge of the dungeon to steal a piece of treasure and escape unharmed, much to the delight of the crowd.
Teen Supervillain, Vamp: She went to a lot of effort to set up a truly epic practical joke on Phase but called it off at the last minute when she realized Ayla was already distraught over something else.
Supervillain, Imp: She seems to keep getting into situations where her good nature shows through past her criminal history, first with Headrush, then with Mischief, saving them from harm.