If I have to say what made me cry the most were:
Kanon: [Makoto route spoilers]The scene where Yuuichi tells her favorite story with Makoto sitting with him as her life force slowly drains her away.[Shiori route spoilers]Shiori had asked Yuuichi if it was alright for her to cry despite her weakening body that she only had months to live her life to the fullest.
AIR: [AIR route spoilers]It was the scene with Misuzu crying to Haruko as she runs up to her being her true mother and embracing her, as well as the death of Misuzu.This is when ‘Aozora’ was playing in the background and it made me cry a lot when listening to it for the first time during that scene.
CLANNAD: [After Story spoilers]Nagisa’s death, the flower field scene with Ushio, and the death of Ushio.
Little Busters!: [LB Refrain spoilers]The parting with the boys as leave one by one as Riki says goodbye to each of his childhood friends, Komari giving her one set of ribbons to Rin for the second time where Rin remembers the good times she spent with each LB members, and the bus accident scene where Riki and Rin needed to act decisively to save everyone.
Rewrite: [Kotori route]The death of Chibimoth, the scene where Kotori’s ‘familiar’ parents were left to defend Kotori and Kotarou as they retreated, and the last scene where Kotori was struggling to save Kotarou from dying.[Shizuru route]The dialogue as Shizuru writes in her diary where she lives within the city of stone as Kazamatsuri had already fallen and the hardships of the people as they were managing how to live their lives.[Moon route]The moment where Kotarou was able to recall his memories of each of the heroines and brought them back to the Moon like the old times they used to spent together as the Occult Research Club.[Terra route]Kotarou and Luis when risking their lives to save the children of Gaia as they were trying to escape from the summoners and Luis had to stay in order for them to escape, as well as Earth Kagari embracing Kotarou in sending him off as she reverts into a plant.
Planetarian: [VN spoilers]The projection with Yumemi narrating the starry sky as the Junker is taken into a world of wonder and amazement of how mankind had traverse among the stars despite global issues concerning the state of the Earth, as well as the death of Yumemi.
Angel Beats: [Episode 10 spoilers]Hinata confessing to Yui that he would want to marry her knowing the circumstances of her body already paralyzed from the waist down to the point he would spend the rest of his life with her.
EDIT (7/25/16): Angel Beats: [Episode 13 spoilers]The graduation scene, the last scene where Otonashi confessed to Kanade as ‘Ichiban no Takaramono’ (Original Ver.) was playing, and the scene when she disappeared in front of him as Otonashi cried.