The second half of episode 207. Momoka's mom promising to come visit before the last cherry blossom falls from a tree, Keroro does his best to keep them from falling, but of course he fails. Then a storm rolls in, and the platoon, plus the Hinata siblings do their best to keep a protective fort around it...and fail again. Then Fuyuki remembers the letter her mom sent, and Momoka finds her under another tree, still in full bloom, and both are happily reunited for the day. The real heartwarming moment comes when we find out why this one tree is still in bloom. Momoka's dad superglued the leaves to the tree, and we get this quote from the narrator, a cute play on the Running Gag of him naming whatever astronomical sum went into paying for the Nishizawa family's schemes:
Narrator: Price of the superglue used by Baio: Priceless.
Episode 229. Kululu blows the entire month's invasion budget to save Saburo when the latter attempts to pull off a Heroic Sacrifice.
Most of the second movie, but especially Natsumi's flashback to Aki finding her when she got lost at a store. The fact that said flashback is what triggered her out of Mind Control is a bonus.
And that flashback was triggered by Keroro, of all aliens!
Pretty much anytime Keroro and Fuyuki just hang out as friends, such as the manga chapter where Keroro and Fuyuki visit a roadside rest stop for aliens.
The Valentine's Day episode. You have to love the normally-Oblivious to Love Fuyuki's glee at seeing the chocolate Momoka made for him, after his disappointment on finding the gifts he'd been getting all day were meant for his sister.
Episode 129. The season arc was that the platoon were sent a timer from HQ that counted down the time left to invade Pekopon. In this episode, the timer had counted down a week too early and unlocked itself to reveal an adolescent Kiruru prototype, called Kiruru Dot. The rest of the platoon are understandably wary of it , afraid that it would become as dangerous as the original Kiruru, but Keroro was the only one to insist that he was different and harmless, even going so far as to name him Mash/Mashiu and let the little tadpole weapon play with his Gundam. (Which coming from Keroro is an Extremely big deal.) Keroro repeatedly refuses to let any harm come to Mashiu, even going so far as to protect Mashiu from HQ, who ordered the Platoon to hand over the faulty prototype so that it can be destroyed and leave Earth. In the end everything turns out alright for the platoon and Mashiu leaves with the mothership, with Keroro chasing after him and telling him to come back, scared that he'll be destroyed.
Volume 20 in the comics has its fair share. Kululu himself even gets a few.
The thirteenth ending song, "Bokura no Aikotoba" (Our Password), is just overflowing with heartwarming. There's a reason it was played in the background during the anime's final episode!
The three-legged race in Episode 26.
Giroro's interactions with the kitty that lives in his tent.
Natsumi accidentally drops her gloves into a campfire Giroro had made, and so he spends the chapter getting advice on how to make a new pair for her. The conflicting advice he gets makes it seem like it's all going to blow up in his face, but in the end, Natsumi really likes them, and it's just a cute scene altogether.
Kululu in the manga gets one in chapter 117 after it's revealed that Mois has been repressing her urge to destroy the planet. All it takes is one panel of him working alone in his lab to realize how empty it is without her and orchestrate a meteor falling to Earth just so that she can destroy something and be freed from her pact. In the same chapter Tamama, who normally hates Mois' guts, stays by her side while she sleeps in the Angol Crystal.
The third movie has a lot of heartwarming scenes such as Giroro and Dororo's rescuing Natsumi and Koyuki from Dark!Keroro's brainwashing, the gang's handling being trapped in the super anti barrier which makes it so they can't see or hear each other, and, of course, Fuyuki and Keroro's friendship scenes which are strong enough to make the Big Bad pull a Heel-Face Turn. There's also a cute scene where Mois cheers up Tamama who had been defeated by an enemy and didn't have Momoka around due to her still being brainwashed.