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Tear Jerker: Sgt. Frog
The Season One Finale (and the manga equivalent, "The World's Smallest Invasion") is probably one of the biggest. It would be hard to come up with a more painful way to retouch upon everything shown in prior episodes.
Of special note is when Dororo and Koyuki say good-bye. Koyuki has been the only true friend of Dororo's and the only one who's never forgotten him, and now he must say good-bye. Their hug seals the deal.
The first movie, all the human/Keronian partners breaking up and everyone's subsequent reactions. *sniffle*
Keroro and Alternate Universe Fuyuki parting ways in episode 205. A surprisingly, and rather strikingly good, tearjerker moment.
The ending of episode 262 has the potential to start waterworks too. We have Keroro hurrying to the station to catch his mother before she leaves on her flight home, to apologize to her for hurting her feelings. He doesn't get there in time.
The Season Two Finale with the Garuru Platoon. The rest of the Platoon's been taken out and Keroro's now Brainwashed and Crazy and ready to take over the Earth. Fuyuki runs up to him and begs for him to stop, screaming for him to come to his senses. It works.