In Happy Tree Friends, all episodes featuring a romance end poorly for the couple. This is most notable with the Official Couple, Cuddles and Giggles, who have the most deaths in the series, and have not survived a single date...until I Nub You, where they were used as a Beta Couple for Petunia and Handy. The latter pair died horribly, but Cuddles and Giggles survived.
Petunia and Handy are pretty cute themselves in the episode, and even manage to "hold hands" by (somehow) tying the ends of their bandages together into a ribbon.
Any time Pop and Cub both live in the same episode.
And any episode in which Pop tries valiantly to rescue or save his son from harm.
Even one of their deaths can be considered a more twisted version of this. In Easy For You To Sleigh, they die probably the most peaceful and painless death in the show: falling asleep and dying from carbon-monoxide poisoning while Pop is reading Cub a story. True, they're still dead, but considering the usual deaths in the show it's downright merciful.
"A Handy Nanny". This is the first real Pop and Cub-centric episode where BOTH of them survive. All Cub suffers is a slight bruise from falling off a table and Pop is completely unharmed. The real moment is at the end, combined with a little bit of Squick, when Cub is napping in his crib after Pop comes home from his bowling tournament. After Handy is shredded up by the knocked over fan, the camera irises in on Cub fussing and starting to wake up. You THINK the bowling trophy is gonna cause his death somehow, but instead Pop just gives Cub his pacifer and he suckles on it peacefully. The squick comes in with Handy's eye being stuck to said pacifer, but still it's the first time Pop and Cub have had a whole episode to themselves and came out alive. (Although And the Kitchen Sink IS debatable in that aspect too)
In Party Animal, Flaky throws Flippy a surprise party. When presented with the cake, he cries a Single Tearof gratitude.
It's easy to miss, but Flippy's myspace page states that he loves chocolate chip cookies. When we see Flaky baking the cake, there is an enormous plate of chocolate chips among the ingredients. Cue Fridge Awwwww.
Also, in Without a Hitch, Flippy constantly wants to help her, despite her obvious avoidance.
Lifty and Shifty have a long history of cheating and stealing from everyone, but Lumpy in particular. So when he sees them go flying by in a runaway cart on his death trap of an amusement park ride, what does he do? Hop on a handcar, chase them all over the ride until he sees the end of the tracks looming, then grab onto a string of flags and flip overhead into their cart, pulling all three to a stop at the very last second. Their reaction cements the moment as a CMOH.
Lumpy's determination to save his pet elephant in Junk in the Trunk. It helps that this is one of the few aversion this series has of Shoot the Shaggy Dog.
Even though The Mole's literal blind date became Lumpy by mistake instead of Giggles, and The Mole accidentally caused Lumpy's scalp to be sliced off early on, it was very nice of The Mole to take his date to some nice places such as the drive-in movie theater, the restaurant, and the Lookout Point even though he wouldn't be able to see those things himself.
The ending of "Class Act", where everyone joins hands and sings "O Christmas Tree" together (except Flippy, who was triggered by the carnage in the actual school and was too busy stabbing someone), despite most of them being severely injured in some way. Then the school explodes and kills everyone.
A couple blink-and-you-miss-it examples from the aftermath of the school's carnage; Mime is trying to comfort a badly charred extra, Splendid has shown up presumably to try and help everyone and Shifty is trying to help out his badly injured twin.
In "As You Wish", Lifty and Shifty hugging each other twice in short succession: first after Lumpy saves them from falling to their deaths, then when their wish for riches comes true. With all the rivalry and betrayals you usually see between the twins, it's nice to see them show some affection for once.
Also, them helping out Disco Bear with his bald problem in Easy Comb, Easy Go. Possibly the first instance of the raccoon duo making money honestly.
There's also the time when, in Happy Trails part two, they invite the surviving tree friends on an inflatable raft. It doesn't end well due to a certain Prickly Porcupine popping it by accident (and even worse in that they were the only ones who don't survive the swim back), but for the two selfish characters that would do anything for a quick buck, it is a nice surprise to see them genuinely charitable.
In "A Concrete Solution", after they accidentally run over Lumpy, their immediate response is to grow concerned and try to help him, Shifty pushing at his chest and Lifty holding his arm up. Sure, they steal his wallet immediately afterwards, but for a moment, they cared to help someone in need.
In "A Vicious Cycle", Evil!Flippy possesses a tricycle and, after killing Lumpy, Disco Bear and Pop, lets Cub ride him, not even attempting to attack him. This shows that, while Flippy in his flipped-out state might be the evilest character in the show (excluding Lifty & Shifty - and even then, they have moments where they show they're not complete jerk-characters), he Wouldn't Hurt a Child.
And there's the implication that Evil!Flippy only kills those who he deems can fight back (like sparing Handy in By the Seat of Your Pants and a bloated, poisoned Flaky in Party Animal).
Meta example. After no new episodes since 2014, the "Still Alive" trailer states there's gonna be 5 new episodes in December!
Lumpy comforting a terrified Flaky with a balloon animal in 'From A to Zoo'. Sure, he made it out of Cuddles' eye, but it's still nice that he went out of his way to make her feel better, even picking her up and carrying her while patting her back in a soothing manner. Plus the little smile on Flaky's face as she looks at her balloon [before noticing what it really is] is just adorable.