This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / Assassin's Creed I
The first Assassin's Creed game has a Tear Jerker, but it's for one of Altaïr's victims, all of whom are undoubtedly evil men. Having said that, two of the victims carry rather sad journeys.
Garnier is a soft spoken man. In his justifying speech, he says that he's trying to free his patients from their own minds (by admittedly brutal means), and is totally graceful in death unlike so many of his brothers. Even being firm in his conviction that he was helping them, saying "It's not what I believe. It's what I know."
Also, in an unusually sad example of Jerkass Has a Point, Garnier reveals while he lies dying that a good number (if not all) of the Hospitalier guards are former patients of his that he did manage to cure, but they only stay sane by taking medicines that he... Apparently didn't think to teach anyone else how to make. He claims that without him alive to make their medicine, they'll got right back to being the miserable (and incredibly annoying) lunatics he scraped off the streets. Guess what happens to the number of madmen in Acre after he dies.
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 Altaïr 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 Altaïr 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 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 little 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 Altaïr will grow over the years and how their friendship ends, you can't help but think that he deserved this less than anyone else.
As annoying as the beggars and lepers can be, they can serve as a painful reminder of how tough times were back then. It's even worse if you revisit the game after playing the second game and realising you can't toss coins this time.