Later, the Dreamweaver is shown to be crying because she was actually regretful for being a puppet to the Master, whose real name is Exos. After she and the hero escape from him when he tries to kill them, she thanks him/her for saving her life. This also counts as a Crowning Moment of Heartwarming.
The "Chaos Scars" cutscene also counts, seeing as how the Chaotic Troll boss was actually Khasaanda and Krellenos' brother, Antiphuus, Chaorrupted by the ninth Lord of Chaos. The hero knew that he was Chaorrupted by Chaos anyway so he/she had no choice but to kill him, and the fact that Khasaanda cried over Antiphuus' death is very sad indeed.
The scene with Lady Vayle and her brother's Spirit Orb during Vayle's ending in the Doomwood saga.
Veddrian's farewell to her ghostly sister Veddris in the final scene of the Bludrut mid-week release.
The moment in Doomwood II when Sepulchure throws himself in front of Gravelyn to protect her from Drakath's attack, thus making this the second time he's been killed by Drakath. Made even sadder when Gravelyn then has to purify her father's Doomblade to save everyone — and in so doing destroy all that remains of him.
The Bittersweet Ending of the Frostval 2012 event. Quetzal, the great beast that Kezeroth wanted to use to destroy Lore, is dead, and Kezeroth has been frozen back in time for at least 26,000 years because Athon, your Chronomancer ally, used all of his power in a Heroic Sacrifice to save the Hero, Frostval, and all of Lore. But while the Hero has done the impossible, he or she doesn't really feel like celebrating due to Athon having to give his life to stop doomsday from befalling Lore.
The Chaos Wedding event on September 2013. It has been confirmed that King Alteon will be our 12th Chaos Lord. The next part makes it worse: Brittany was killed off by the Corrupted King Alteon.
The finale of the Swordhaven saga. Brittany's death at the hands of the King has unleashed the Chaos Dragon, the worst Chaos Beast yet, upon Swordhaven. Because of the Chaos Dragon's initial assault, Swordhaven is in flames. And worst of all, your final battle is against King Alteon himself — and no matter how you choose in the end, you will have to kill him to free him from his Chaos-induced madness. The saga ends on a serious downer — Swordhaven is in ruins, the Alliance is headed for disaster following the fall of the most prominent force for Good, many people are dead, and there will most likely be war as the various candidates vie for the throne.