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Tear Jerker: Baldur's Gate
Baldur's Gate II. Yoshimo's death. The fact that he's the only proper thief in the game is also sad.
Jon Irenicus's speech to Ellesime at the Tree of Life helped to humanise and add tragedy to a character who up until that point had been an unrepentant, sadistic Magnificent Bastard.
I... I do not remember your love, Ellesime. I have tried to. I have tried to recreate it, to spark it anew in my memory. But it is gone... a hollow, dead thing. For years, I clung to the memory of it. Then the memory of the memory. And then nothing. The Seldarine took that from me, too. I look upon you and I feel nothing. I remember nothing but you turning your back on me, along with all the others. Once my thirst for power was everything. And now I hunger only for revenge. And... I... Will... HAVE IT!!
At the end of Throne Of Bhaal, if you're in a relationship with Jaheira, her reaction to whichever decision you make is worthy of the name Tear Jerker.
The ending Where Are They Now stories for party members quite Tear Jerker-y. At least, Minsc's "they're together still, up among the stars where hamsters are giants and men become legend". Viconia's romanced non-ascension ending where her past finally catches up with her and she is denied even the experience of seeing her son grow up by the ever-scheming Lolth and her followers is also liable to make your eyes water.
Kelsey's romance mod can make players tear up every time. Not helped by the almost sobbing of the voice actor.
Kelsey. Tree Of Life. "So let me just say this. I love you. I need you. And I am with you until the end." It's voiced. Cue waterworks!
The Master Wraith in Throne of Bhaal WILL tear up your romance option, but none came close to utter heartbreaking like Aerie. To wit: he conjured an image of her mother, who proceeds to blame her for getting the latter killed by more sadistic slavers, all because Aerie dared to go missing from her. Aerie may be a little too whiny for her own good, but on the other hand, hearing her completely break down sobbing and begging it to stop is just too much.
In the Tales of the Sword Coast expansion for the original game, the resolution of the Werewolf Island subquest is rather tragic. There is one particular character — the friendliest one in the village and pretty much the only one who doesn't hold your outsider status against you — who you can do favors for such as retrieving a cloak and delivering him/her (depending on your player character's gender) flowers. If you pick the nicer dialogue options, the journal entries reveal that you are becoming increasingly fond of him/her. If you offer to take him/her with you to the mainland to start a new life together, he/she will consider it but ultimately refuse out of fear and lingering attachment to the village. That's sad enough. After The Revealthat the villagers are all dangerous werewolves, he/she helps you to evade them and shows you an escape route. Your new friend and nascent Love Interest still refuses to leave and decides to fight the other villagers to buy time for you — and it's heavily implied he/she doesn't survive. The journal entry covering this ends with the words "...I wish..."
There is, however, a mod in the works which will allow said villager to join your party in the second game (and even become a full fledged Love Interest). So a nice Fan Retcon on what would otherwise have been quite a Downer Ending.
Many Bhaalspawns in Saradush don't want anything to do with their heritage and just want to go on with their lives. It's also heavily implied that Bhaalspawns will end up in the lower planes when they die, regardless of alignment and by all accounts, they all die when Saradush is destroyed.
Jaheira finding Khalid's corpse at the beginning of Baldur's gate 2. This is the first time the rather stoic Jaheira breaks down crying. And even if you consider him The Scrappy, it's rather hard to not break down.
A short line from Imoen, after the revelation of her Bhaalspawn power
Imoen: I don't feel like I fit in with the people of the city anymore.