This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / Assassin's Creed IV: Black Flag
Early in the game, when Edward meets the Assassins at Tulum and after saving the captives from the Templar mercenaries who invade the island, James Kidd leads him back the temple and the centre courtard where the surviving assassins have piled the bodies of their brethren and are mourning. Considering that these deaths were consequences of Edward's own unthinking actions which the player participated in, it qualifies as a Player Punch and a You Bastard moment. It also makes Ah Tabai's forgiveness of Edward that much more remarkable and Edward's clinging after money that much harder to stomach.
Desmond's in-game audiotapes, recordings he did in the spare time he had in Assassin's Creed III is deeply sad, bringing forth the point that he was just a young regular guy whose life was sacrificed by things set into place centuries in the past. Also his reflection on his father, his friends and on the memories of his ancestors, especially Connor whose story he finds painful shows how he's matured. As well as his reflection that the past wasn't shaped by idiots, but intelligent men and women whose best efforts ultimately had little effect.
A document you can retrieve through hacking reveals that Desmond's friends in New York put up missing person posters after he was kidnapped. Not only did they care enough about him to do so, but they'd never see him again, or find out what happened to him.
One of the tapes has Desmond recounts a story of how he was expected to sneak up on his father (a cold, distant and distinctly not very friendly person); he waited hours before finally creeping into his room only for his father to notice him but pretend that he didn't and happily congratulate him. Desmond was furious with this lie but has later come to realize that he was rewarding his patience and, just maybe, his mentor just wanted to be is father for that brief moment.
There's also what became of Desmond after the credits of Assassin's Creed III rolled. Instead of a proper burial or even a tearful send-off, Desmond's corpse is found by Abstergo researchers and autopsied on. The man who in a sense saved the world was effectively reduced to a mere footnote by the Templars as Sample 17. It's as if Desmond was able to check out of life, but in the end could never leave.
Also on a meta level, the fact that the Templar are using Assassin descendants to make a game full of false representation out of the lives of actual assassins is especially heart-rending. Humiliating their enemies after their downfall in this manner is not unlike what Joffrey did in Game Of Thrones.
The death of Blackbeard, Edward being so close by yet unable to help.
Hell, the music makes it even worse. The sounds of the battle raging are completely muted, with this track being the only audible thing. It really hits that Kenway lost more than just an ally.
"In a world without gold, we might have been heroes!"
After Mary Read dies, Edward takes Drowning My Sorrows to the extent that even the loading screen representation is groggily stumbling about with a bottle in hand.
Edward's last words to Mary are especially heartwrenching.
Edward: Damn it, you should have been the one to outlast me.
Mary: I've done my part. Will you?
Edward: If you came with me, I could. Mary?
Mary: I'll be with you, Kenway. I will.
The song which accompanies the scene,"I'll Be With You" amplifies the overall sense of loss in the scene.
Edward's long delayed Heel Realization is very moving because you get that he's really remorseful and understands the consequences of following his obsessions.
Edward: For years I've been rushing around, taking whatever I fancied, not giving a tinker's curse for those I hurt. Yet here I am... with riches and reputation, feeling no wiser than when I left home. Yet when I turn around, and look at the course I've run... here's not a man or woman that I love left standing beside me.
Related to this is the fact that after Black Bart's mutiny, Edward's time in prison, Adéwalé quits as your quartermaster. This loss is reinforced by the fact that in the endgame, Anne Bonny is still your quartermaster. The fact that it was Edward's, and the player's, own selfishness and bad behaviour that played a role in Adewale joining the Assassins hits you and you miss having your friend on the next raid. Even Edward joining the Assassins doesn't change that and while they are amicable you sense that they aren't close anymore, you feel you drove a good friend away, feel just like Edward.
At the end, when Edward sees his dead friends happily drinking and smiling at him. Especially since Anne sings ''The Parting Glass'' in the end scene. Especially the lines,
"Since it falls on my lot/That I should rise and you should not..."
One of the hunts for a Templar has you teaming up with Assassin Rhona Dinsmore, who eventually helps you lure out Hilary Flint so you can kill him and take his key. However, Rhona is noticeably reluctant to do so — specifically, she plans to play distraction so that it's Edward who does the killing — and it turns out that, while on opposite sides, she and Flint were somewhat in love - and he dies in her arms.
The flashback where Edward leaves for sea is the first scene where we get a glimpse of a more vulnerable side of him as he quietly laments how this is the time where he truly needs his wife's faith and blessing. It's also sad because you can sense that his wife still loves him and it hurts her to do this, but she doesn't want to be his enabler anymore. The fact that she dies and Edward Never Got to Say Goodbye is deeply sad in itself, more because Edward had finally changed and wanted to do right by her, only now its far Too Late. Edward's expression when he gets the latter with the Wham Episode that his wife is dead and is survived by a daughter he knew nothing about, is filled with regret, realizing that he failed her.
The epilogue reeks of this for anyone who played Assassin's Creed III and especially those who read Forsaken. Despite the game ending happily with Edward and his children, in later years, Edward will die at the hands of Templars, his daughter will be sold off to slavery, and his son will become a Templar. This is Lampshaded in the game, one of Desmond's conversations has him quoting Orson Welles:
"If you want a happy ending, it depends of course, on where you stop your story."
Finding the remains of the Jackdaw in Freedom Cry. While he has left behind his days of piracy, it's clear Adéwalé is sad to see his old "country" in shambles at the bottom of the sea, only able to salvage the figurehead.
Even worse in Freedom Cry than that is the mission where you attempt to liberate another slave ship. You eliminate two of its escorts, only for the remaining one to open fire on the slave ship itself. Then, Adewale goes on board and tries desperately to liberate he surviving slaves, personally breaking their chains and trying to get them out, all while surrounded by the dead and dying. Then, to make matters worse, the ship begins sinking and Adewale must escape, even as the screaming bodies of the slaves he just freed plummet pass him. He then gets to swim past their drowned bodies to reach the surface, only to end up trying to climb out of the ship, past even more slaves still chained to the deck, many of them struggling and writhing as they're pulled to their inevitable doom. Really, the whole sequence is as horrifying as it is heartbreaking.
While he may have been a complete Jerk Ass, there's something pitifully sad about seeing a mentally-broken Charles Vane wasting away in prison.