Tear Jerker / Guyver

• At the top of the list is Sho and his father, against their wills, one by Barcas' mind control, the other by the Guyver's self-defense mode fight and it ends with the Guyver Mega-Smashing his own father. But the 2005 anime cranks it up to eleven, because it gave much more time to Mr. Fukamachi and strengthened his and Sho's relationship.
• The men of Takeshiro Village being unwilling Zoanoid sleeper agents who forcibly transformed and attacked Sho and Mizuki (Along with Tetsuro, Murakami, and the Onumas in the OVA series.) Agito then slaughtered them and said that it was the only way. What especially twists the knife is that a little girl witnesses her father transforming and tries to reassure him that he's just sick and he'll be okay. There's then a quick close up of her face and she's never seen again. (She ran away in the OVA series, but it's unclear if she escaped unharmed.) It's also unknown if all the other women and children successfully escaped or not.
• Dr. Odagiri taking Guyot's gravity bullets to save Murakami and then Murakami's death at Guyot's hands both cranked up higher in the 2005 anime.
• A pretty close second is seeing the Creators/Uranus leaving Archanfel behind. The expression Archanfel makes when he cries out 'Then why was I created!?' is a combination of sadness, anger, betrayal, and fear certainly not just humanizes Archanfel but is a very powerful image in itself.
• It's rather heartbreaking to watch Waferdanos and Li Yentsui do their damnedest, and at the cost of their lives, to make sure Barcas survives and escapes with an item Guyver III will do anything to get. And ultimately they fail. Even if one roots for Agito, it's hard not to feel sorry for them.
• Hayami saving Aptom's life by freezing his mind-controlled body to the ground so that Sho can Mega-Smash it, and then allowing the last fragment of Aptom, finally free of Khan to consume his body to re-grow, telling Sho that he's grown stronger and dies with a smile
• The thought of how many friends, siblings, lovers, and children wept when their loved ones got up in the middle of the night, transformed, and all merged together to create Khan's one winged angel form and never came back...
• Test Type (also known as Malmot in some translations) The very first Zoanoid we see. All the guy wanted was to be human again to return to his family, so he goes and escapes from Cronos with the units to hand them over to Agito, while having the false hope that he could become human again. Turns out Agito tricked him and because he left before the process could be complete, he can only live for a week. It's sadder in the 2005 anime, where we see one last shot of his family photo after his death.