In the manga, when Shin and Mickey fly over a Bedoin camp that had been slaughtered by anti-government troops. Shin was mortified, particularly at the sight of a dead woman clutching a dead child.
In the manga, we see a flashback of Saki weeping after Soria dies giving birth to Rishar. He lovingly holds the newborn Rishar with tears running down his face.
In the manga, Hoover sharing the story of the training accident that killed several pilots under his command. During a NATO training exercise back in Europe, Hoover flew too low into the sun. The pilots flying behind him in formation mistook the sun for his afterburner and crashed into the side of a mountain.
Hoover: I killed them.
In manga published in Animerica, Saki is deeply distressed as an injured Rishar clings to life in the Area 88 infirmary. Saki admits that he "truly will be alone" if Rishar dies.
In the manga, Tracy's exposition to Mickey on the tormented man he'd become after the Vietnam war.
Toward the end of the manga, Greg's death scene is a major tear jerker. After his A-10 crashes near Asran City, he finds a little girl whose mother has just been killed in the fighting. The crying girl accidentally shoots him with her family's gun. Greg is not angry, and he tells the little girl that she will be a good mother someday. He dies peacefully, smiling.
Near the end of the manga, a dying Abdael tells Saki about the real reasons why he instigated Asran's civil war: to develop Asran's medical technology through foreign capital so that a treatment for Soria's blood cancer could be discovered.
Also, Saki's suicide near the end of the manga, after Abdael reveals the truth about Soria and the roots of the Asran civil war. Saki admits that the Asranian people would not accept him after his role in the civil war. He carries Abdael's dead body into Soria's tomb and shoots himself as a horrified Shin looks on.
In the manga, Kanzaki's account of his mother's suicide is a tearjerker or a source of nightmare fuel, depending on your perspective.
Near the end of the manga, Mac learning that his daughter Miriam has died.
Boris's death in the anime and manga. The manga is more heartbreaking because both Shin and Mickey are screaming at him to save himself, and he doesn't.
In the OVA, seeing Shin burst into tears in his quarters, lamenting his involuntary servitude at Area 88.
After one of the final battles of the manga, Mickey and Sela die. Sela runs over to his F-14 after it crashes on the runway and finds him unconscious and bleeding. She kisses him just before the wreck explodes, killing them both. Even more tragic is the fact that Mickey's F-14 was damaged because he'd just shielded Sela's jet from Mac's gunfire.
Mickey has the unfortunate problem of fighting Patrick Reed, one of his wingmen back in Vietnam War fighting for anti-government forces as a mercenary. After defeating him, Patrick tells Mickey that he wants badly to go back to Oklahoma, highlighting the problems military personnel back in regards to integrating back to normal lives.