Actually, no scratch that, Yukikaze is filled with moments like this, including Yukikaze ejecting its pilot before shooting itself and telling him "good luck", and the very ending of the series where Lynn Jackson sees an image of Rei standing on the hillside with Jack, when he really can't be there.
Tomahawk John's death in both the anime & novel. Begging Rei to please reassure him that he's a human.
Numerous moments from the first novel.
Rei's first Guy in Back, an unnamed EWO (electronic warfare officer). When Rei destroys the unknown Sylph in the intro, debris from the explosion badly damages Yukikaze. The EWO ejects while Rei attempts to regain control of Yukikaze. He succeeds and manages to return to base. He is then told at his hearing that the EWO was found by a search and rescue team... or rather, his body was found, devoured by native Faery wildlife.
Everything about 2nd Lt. Mamoru Amata. The man has perhaps the worst job in the FAF, he is treated like crap by his superiors, he has no future on Earth, he is destroying his body with his constant drinking but he must or else he'll freeze to death. And then out of the blue he receives an Order of Mars medal, something that is only given to those who truly go above and beyond the call of duty (think of it like the American Medal of Honor). It changes his life in all the worst ways possible: his superiors still think he's a joke and his colleagues resent him for it. When by chance he talks to Jack Booker about it, he finally breaks down and begs him to find out who made the decision to give that cursed medal to him. But in the end, it doesn't even matter. He gets killed by the SAF AI to prevent Yukikaze from crashing into his snow grader during a snowy landing.
Captain Hugh O'Donnell's fate. He doesn't get to beat Yukikaze in a fair fight during the Fand II test flight, only winning because of a technicality. Then the JAM attack. Yukikaze takes control of the Fand II and uses its armaments to fight off the attackers, but the extreme-G maneuvers she makes the Fand II pull end up killing O'Donnell. Back at base, O'Donnell's girlfriend Lt. Emery goes through a major Freak-Out when she finds his dead body. She draws her pistol and shoots the corpse, reasoning that Hugh couldn't have been killed by a machine: he had to have been killed by a human. Major Booker is wracked with guilt, wishing that if he'd listened to Rei and allowed him to pilot Yukikaze instead of sending her up unmanned, this wouldn't have happened. Rei disagrees: if that had occurred, then the only difference would have been that the JAM would have destroyed both Yukikaze & the Fand II. He writes off O'Donnell's death as just another casualty in the war, not giving a damn about the heartbroken Lieutenant grieving him. It's even worse as she had just become his fiancee; he had promised her this was going to be his last test flight and that they'd be married in two months.