Iwata protecting Ropponmatsu II from a robot bomb, this is heartwarming because it was Iwata who found her the most annoying in the beginning of the episode yet he was the first one to jump to her aid.
The show's canonical Grand Finale, episode 25. Excel and Ilpalazzo end up together after she helps him rid himself of his Superpowered Evil Side, while Hyatt is last seen in the care of Watanabe. Also, Pedro and his son get help from the spirits of Nabeshin and other dead characters in a Dragonball Z-style parody and defeat That Man, saving the world, meaning Pedro and his wife can finally be reunited.
Also in the previous episode, Menchi actually coming to befriend Excel and help her out. Considering how dysfunctional their relationship has been in the past (since Excel, you know, always brings up the possibility of eating Menchi), seeing this happen is indeed heartwarming.
And in both that episode and the one before that, we have scenes where Hyatt is worried because Excel is gone and futiley asks Ilpalazzo permission to go look for her. It's such a sweet reinforcement of what True Companions Excel and Hyatt are.
Late in the manga, Matsuya kissing the very-much-alive Iwata during the penultimate chapter, then beating the shit out of him in a tearful rage hits a rare hat-trick of heart-warming, tear-jerking and funny.