In the 2005 anime the final conversation between Sho and his father. The two had trouble talking to one another when the latter found out of Sho's 'ability'. The two finally spitting out some father-son words pulls the heart strings strongly.
Another but outside the manga. After the issue showing Murakami's death readers began send paper cranes to Takaya in honor of the character.
Yet another from outside the manga. Apparently of group of fans are trying to assemble a quilt for Takaya as a 'get well' gift due to his recent illness. If it's completed it'll be a crowning moment of awesome as well.
Hayami's goodbye to Sho and Aptom as he sacrifices himself to save Aptom, just because he seems so at peace.
After very, very long long arc involving rescuing Aptom, growing stronger both in ability and character, and defeating Draglord Khan with the Gigantic Exceed, Sho gets rewarded for all his pain and suffering by finally sleeping with Mizuki. Considering what a downward spiral Sho's life as been since finding the Guyver unit, it's just great to see Sho and Mizuki getting to be happy.
In the 2005 anime there is the touching seen between a recovering Murakami and Mizuki. While peeling an apple for him she explains that Sho always acted like a girl and she preferred more athletic guys. Murakami is amused by says that he was more like Sho than Agito and loved to take care of animals and was a cry baby. It starts to make Mizuki giggle. Aww.