In Metal Gear Solid 2 where Otacon's younger sister Emma dies. He cries and wails in misery, unable to focus on the mission at hand. Snake then fills his heart with courage once more in a brotherly embrace. As the two warriors leave the hacker, Emma's parrot mimics her, saying that she missed him, sending him once more into a tide of grief. The whole sequence is heartrending.
Not to mention Otacon has to decide to leave her corpse on the Big Shell, which is going to flood. When the camera shows the area when the flooding is happening, though, I don't think I saw her body...
If Otacon wasn't The Woobie already, he damn sure is now.
Worse in the fact that Otacon, unlike most others in the series, was never a soldier or a fighter. He was just in the wrong place at the wrong time.
Any time Otacon cries is made even worse by the acting. Unlike almost any other performance, it actually sounds like someone breaking down. It's not a single tear, it's not controlled sobbing, it's wailing and screaming and crying like a child. Christopher Randolph puts everything into the scenes where he has to cry, and it is heartbreaking.
Emma: I remembered my brother giving me a piggyback ride. I was sleeping with my ear against his back. I could hear his heartbeat.
Raiden: Sounds like you two were close.
Emma: We were... back then.
It also doesn't help the fact that Emma and Otacon hadn't seen each other in years, and then when he finally sees her again, she is stabbed by Vamp just before she reaches him and dies in his arms.
Raiden: What if I've never really met her...? If the Colonel is something that I partly dreamt up, then... everything I remember about her could be...
Olga's story is pretty sad. The Patriots took her newborn and forced her to secretly take down her comrades in order to help Raiden survive, otherwise they'd kill the baby, even at the cost of her own life. Luckily, Snake goes to save the baby after Solidus is defeated, and by five years later, he and Otacon have raised her themselves.