Gremio: Young Master, can you hear me? I'm sorry I can't protect you anymore. ...But now that you've grown up, you no longer need my protection. Young Master...You make me proud. I wish Master Teo could see you right now.
Gremio: Young Master. I think it's time to say goodbye. I can't see anymore. Young Master. I'm proud of you. Promise me that you'll always follow your heart. That is my first, and final... request...
To make this even more heartbreaking, listen to the Drama CD version. Tir spoke, and Kenichi Suzumura's performance as an utterly heartbroken, desperate and helpless Tir screaming for Gremio to just frickin' open the door is just heartbreaking.
The scenes after the duel between the Tir McDohl and his father make quite an impact.
Ted's back story of his village being attacked by Windy along with the village's theme song may make you reach for your tissues. Not to mention his own death.
Okay, so it's fairly Narmy in retrospect, but I just broke down the first time I played Suikoden all those years ago and got to Odessa'sHeroic Sacrifice. The later Player Punches were just as bad, especially when it was finally made clear that it's the fault of your True Rune that everyone you care about is dying. It's known as the Soul Eater for a good reason.
Seconded. Odessa really had a good future and looks really cool... if it wasn't for her womanly instinct to kick in the wrong time and costed her life. It's even worse that her last words were basically telling Tir that despite Flik's clingy attitude on her, she cared about him a lot.
Viktor: Are you all right, Odessa?
Odessa: C-come...you can come out now. Quickly! You must run...
Little boy: O-OK.
Gremio: Lady Odessa! You're bleeding!
Viktor: Odessa! What have you done? Without you, the Liberation Army...
Odessa: I'm...so sorry, Viktor. It appears... I've chosen to be a woman...rather than commander of...the Liberation Army. I couldn't let that child die. I'm a failure...as a leader...
Cleo: Don't talk, Odessa. You'll reopen your wound!
Odessa: Tir, will you...come here? I have...two requests. First, give this earring...to a fellow called Mathiu...in the village of Seika...
Viktor: Stop it, Odessa. I don't want to hear any final requests!
Odessa: Viktor...thank you, but...I know the end is near. Tir, take it...M-my other request...Please throw my body...into the stream there...
Gremio: What? But why? I can't do such a horrible thing.
Tir: I can't.
Viktor: He's right, Odessa. Why do you ask such a thing?
Odessa: If the Liberation forces find out I'm dead...the Movement will lose faith and die...That is why you must keep my death a secret. The tiny...newborn hope...must be kept...alive...
Tir: I can't.
Odessa: Look, Tir, this is blood...my blood...You are not aware of it, but a lot more blood is being shed by the innocent...at the hands of the Imperial Government. You must put an end to it. Even if I die...If my hopes remain alive...I can be proud of my life. My blood...
Tir: As you wish.
Viktor: Tir! How can you...
Odessa: Thank you, Tir. You understand me, don't you? Viktor...if the Liberation forces find out I'm dead...the Movement will lose faith and die. That is why you must keep my death a secret. Our tiny, newborn hope...must be kept alive... If you...ever see Flik again, tell him his kindness always saw me through hard times...Well...it appears the end is near...Tir, I hope that you will be able to see the Free World that I was...never able to...
The sequence after the last boss is a sequence of Tearjerkers, from Barbarossa's confession to Windy of his desire to save her from her sadness and their subsequent suicide to Viktor and Flik's apparent deaths (not so much if you play II, but it counted before II's announcement) to, worst of all, Mathiu succumbing to his wounds and finally passing away just as his sister's dream is realized.
Mathiu: Master Liukan, those voices...Have we won?
Liukan: Yes, undoubtedly.
Mathiu: I see. Master Liukan. I despise war. I always felt that to take a life of another, for whatever reason, was wrong. And yet, I became a military strategist and took many lives. Did I do the right thing?
Mathiu: Perhaps I should have remained in that village, fishing in my idle moments, until my death.
Liukan: Master Mathiu...the answer to that...
Liukan: Are you asleep now, Master Mathiu? May you rest in peace. You have accomplished so much in your life.
Lady Anabelle's unexpected death done by Jowy, the main character's best friend in an act of "betrayal".
When your sister Nanami falls (whether she dies or not is up to whether you recruited all 108 stars), it is a huge Tear Jerker moment, especially when she tells the hero how happy she was to be his "Big Sister". Also, Pilika's plotline is a huge Tear Jerker. She loses her village and her parents, is rendered mute when she is nearly butchered by Luca Blight, is apart from her beloved caretaker Jowy for a long time, and in the end, there is a scene where Jowy tells Pilika than when he leaves, its "goodbye forever". Pilika tells Jowy to hold her like her father held her.
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.
Losing Lulumay 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.
Then there's the sequence in Suikoden III where you finally catch up with the Flame Champion... 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.
Bring Futch and Viki to the final battle against Luc, and it was pretty heartbreaking too when Viki asks one last time if they're fighting her previous ally, and Futch told 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 I 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.
Troy's loyalty to his empire, even until the very end of his demise.
Seeing Ted from Suikoden I and know his reluctance to get close to anyone.
If you aren't cursing his stupidity, some of Snowe's moments can be pretty depressing, like how he completely fails to get WHY everyone reacts so poorly when he's trying so hard. Highlight has to be his breakdown when he's driven out of Razril by an angry mob shooting fire arrows.
Snowe: Everything I've done was to protect you! Why am I being blamed for it?