Final episode. When everything looks bleak at the loss of the other Taroses and it looks like Momo's going to disappear himself while they're trying to protect Airi and their era, Ryotaro finally makes his wish that Momo had asked of him since episode 1.
Ryotaro: I'm going to tell you my wish. Momotaros:(pause) Let me warn you. I won't hear any wishes that I can't do. Ryotaro: Will you... (thinks back to Urataros and Kintaros pulling a You Shall Not Pass) ...fight with me until the very end? Momotaros:(beats up several Mole Imagin after a longer pause) Your wish... has been heard.
At the end of Ore, Tanjo!, Owner sets it up so Ryotaro gets to see his parents as they leave the hospital with himself as a newborn.
The end of the series, where Yuto thinks Deneb vanished after Kai's defeat, and returns to the ZeroLiner to discover Deneb left him a meal with a note asking him to eat it and keep up his strength. Breaking down in tears, Yuto starts eating, even the shiitake he despises. When Deneb turns up alive, rather than being comically annoyed as usual, Yuto just hugs him.
Ryotaro's own version of the scene is similarly heartwarming, but not quite to the same extent since we see the Taros alive earlier, and acting goofy, which is a little of a Moment Killer.
The arc with the time capsule. The person who contracted it is trying to find it because his deceased wife had buried something precious. At the end of the arc we find out what it is, an old pair of boxing gloves because he gave up boxing to live his life with his beloved. The man breaks down into tears.
Heck Ryotaro, after tying a piece of cloth to the teach next to it while in the past, digs up for him, in the middle of the rain. Hana even helps him dig it up.
The revelation of Yu's identity in Onigashima Battleship might have been a little obvious, but it was still sweet.
In the episode where Kai succeeds in killing Yuuto when he was a high-school student, we briefly glimpse how Oozaki and Miura would have lived if they'd never become infatuated with Airi. Oozaki would have kept on womanizing, of course, but Miura would have found a woman who loved him back. His lone appearance in the episode shows him with his infant daughter, who he clearly loves very much.
Doubles as a tear-jerker when, at the end of the episode, Yuuto's existence is restored and Oozaki and Miura are back to competing over Airi, who still doesn't notice their feelings.
In the episode with the courage test, this troper found it touching that Yuuto was willing to use one of his 2 remaining Zeronos Cards to save Deneb who he thought was in trouble. While he beats him up afterwards, it's still very heartwarming.