Losing Lulu may not have bothered some players, but when you have to break the news to their mother... It's made even worse when Hugo's mother Lucia embraces him afterwards and confesses that as much as she hurt for Luce, she also felt some relief that her own son was still alive.
Learning the Flame Champion's history, how he gave up the True Fire Rune so he can stay with his loved one, only to face the fact that they have very short time to be together.
Then there's the sequence where you finally catch up with him... Or, rather, with his long-widowed wife, Sana, who explains how he sealed away the True Fire Rune and traded immortality for the chance to grow old and die with her. It's heavily implied that the strain of sealing away the Rune sapped so much of his strength that they didn't get to enjoy much of their new life together, to boot.
Bringing Futch and Viki to the final battle against Luc. It's pretty heartbreaking when Viki asks one last time if they're fighting her previous ally, and Futch tells Luc that he'll never forget the times they spent as allies during two liberation wars... as much as a Jerkass Luc was both times.
Viki's newspaper article too. During the events of Suikoden and Suikoden II she used to get refused by Luc when she asks for picnic, only to agree in the last seconds. When even the resident ditz used to remember that Luc used to be somewhat a mere TsundereJerkass... it just gets sad.
Chris encounters her father after nearly 20 years just in time to inherit his rune and see him die.
