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Tear Jerker: Assassin's Creed I
The first Assassin's Creed game has a Tear Jerker, but it's for one of Alta´r's victims, all of whom are undoubtedly evil men. Having said that, Sibrand's death is rather sad. In an eavesdropping event and just before you kill him, you see Sibrand as an incredibly paranoid, vicious man who kills an innocent priest under the belief that he's an assassin sent to kill Sibrand. He's ranting and raving as he fires arrows into the air as you approach, but when Alta´r finally gets him, he quietly begs the assassin not to kill him. It turns out due to the Templars discovering the Piece of Eden in Jerusalem has proven to Sibrand that there is NOTHING after death. No heaven, no hell, nothing, and he's terrified of what's about to come. It puts all his crazy paranoia and ranting into perspective. The knowledge that there is nothing but darkness waiting for him has effectively destroyed Sibrand, long before Alta´r came along. Despite the fact that he's evil, like all the other Templars, when he says 'Nothing waits', it can make one feel bad for him.
In the semifinal return to the present (that is, before the final memory), Desmond wakes up to learn that a group of Assassins is raiding Abstergo. He hears over the radio, however, that Abstergo's guards quickly dispatch them, with little more than the gunfire abruptly ending. Vidic takes this time to gloat to Desmond over how that was (supposedly) the last of the Assassins before leaving. Desmond's Darkest Hour, and by extension the player's, is a moment of muted despair where he realizes that there is nowhere for him to run...until Lucy reveals herself to be an ally of the Assassins, that is.
There is also one for Malik, at the beginning of the game when he loses both Kadar and his arm. The effect is pretty lost on the player at first, as Kadar had almost zero screen time before he died and Malik just got introduced. When the player comes back though, especially after completing the Ezio Trilogy, and is aware how close Malik and Alta´r will grow over the years and how their friendship ends, you can't help but think that he deserved this less than anyone else.