Haley's motive for collecting money. She favoured helping the dirt farmers even though there would be absolutely no reward. Notably, she called Roy out for assuming that she wouldn't want to help them — yes, she likes money, but just because she expects compensation for adventuring doesn't mean she won't help people in need!
Belkar Bitterleaf, a Chaotic Evil halfling who on one occasion used a kobold's head for a salsa bowl, has recently adopted the late Lord Shojo's cat, Mr. Scruffy. While he justifies it by using the cat for a weapon at one point, he seems to genuinely care for it. Then again, he also liked Lord Shojo for being a Magnificent Bastard, to the point of going berserk when Miko killed him. ("YOU KILLED THE WACKY OLD DUDE WITH THE CAT?!?")
Miko seems to have a genuine affection for her paladin steed, leading to a few Pet the Horse scenes, especially her final moments.
Tsukiko seems to be getting one of these in her deluded, but still caring, attitude towards the undead. Then again, since she's a self-confessed necrophiliac, her motherly behaviour towards them might make it even worse.
Gannji and Enor have an ever-so-slightly heart-rending shared Pet the Dog moment during the Gladiator Games, when they refuse to duel each other and Gannji has to persuade Enor to kill him in order to prevent them both being executed.
This moment was so moving it inspired Belkar to have one of his own by releasing a dinosaur into the arena to allow them to escape since their relationship reminded him of his bond with Mr. Scruffy. The carnage that resulted was a bonus.
Richard of Looking for Group has a rather shocking Pet The Dog moment when he saves a child from an explosive blast. The reason? The child wasn't afraid to die.
A more straight example is how Richard seems to like the rabbit the rest of the group jokingly gave him as a mount when he was shrunk. Well, at least, it's one of the few woodland creatures he's run across that he didn't immediately immolate.
Sarda seems to like Fighter more than the other three, probably because he realises that he's actually good as opposed to Black Mage, Red Mage and Thief. For example, in one instance, Fighter asks for a reward (and hopes that it is candy), but Sarda says something about the next quest. In the end, Sarda tells Fighter, "By the way, Fighter, here's the candy." Also, Sarda (after resurrecting Fighter and Thief, who have been killed by Black Mage) states that the Light Warriors are "all selfish monsters who need to die for the good of everyone else." Black Mage asks surprised if that also applies to Fighter, and Sarda answers he isn't. While Fighter cheers, Sarda explains that he still has to kill him anyway. And then Black Mage cheers.
In Girl Genius, volume 12, Tarvek drags a wasp weasel handler, a nest of baby wasp-weasels, and a Jager out of danger, followed by attacking a Wasp Queen — with a wooden sword.
The Ork from Da Real Wurld40k seems to like the grots that infest the character's house. The Dark Eldar chick constantly demands he do something about them, and he seems genuinely saddened when she shoots one off his head. For an ork, he's surprisingly well-balanced.
Rowasu of Juathuur doesn't kill Juinn when he has the chance. Not only that, but he doesn't kill his crow, who ate one of his eyes!
In Goblins, Minmax the Unstoppable Warrior is the first antagonist the heroes face, and his party's slaughter of a goblin village is the catalyst for the Goblin Adventuring Party's formation. He is painted as a mostly unsympathetic jackass who is technically Chaotic Good, but assumes all goblins are just XP fodder. When he eventually meets the Goblinslayer, he is overcome with hero worship. But when he finds out the latter has a sapient snake-woman whom he rapes and tortures nightly for fun, he throws him through a window.
"Saddest story you ever heard. Got to do something to shut him up."
Even the kid's version of Jack Noir gets one. Thanks to Bec's prototyping, he's incredibly loyal to Jade - so much so, that when Courtyard Droll kills her (as per Jack's earlier orders), he takes her to her Quest Bed, more-or-less willingly undoing her death. Jack's sole motivation is to kill everything in existence.
Equius spent most of his time onscreen as kind of a racist, classist prick with an intricate arrangement of creepy fetishes, but managed to get in a few of these, such as building the low-caste Tavros bionic legs to heal his paraplegia. The best example, however, was when he was certain he was going to die accurately, as it turns out, and took a moment to say goodbye to Nepeta and thank her for being his moirail.
Seymour from Nosfera deciding to spare the life of the Medusa Head in front of her children.
In City of Reality, an unnamed villain who's revised the timeline gives a seemingly heartfelt apology to a little girl she's had to Mind Control for her ends and in the original timeline had been forced to kill.
At the end of chapter five, Norbert Olsen from The Overture tucks his favorite daughter Angela into bed. Up until this point, Norbert has either been abusive or neglectful to his other children so it's shocking to see he generally loves Angela with all his heart.