Assassin's Creed: Revelations/Tear Jerker

Yusuf's death. It's unexpected, and is made even worse by the fact that Yusuf is a very likeable character, and does a lot to support and help the player.
Sixteen's death. A double whammy, really. First, you (the player) are led to believe he has betrayed you and started to actively attempt to murder you. Then you discover that this is not the case, and the reason behind all this glitching and Animus Island being deleted with you still on it is actually the Animus itself. And then he sacrifices himself to save you.
- Even sadder considering that Sixteen has been a true friend and guide to Desmond throughout the entire series.
The third Altair memory with Maria's death and Altair's exile
Ezios death in Embers.He finally dies from a peaceful heart attack while his wife and one of his children see him die.Made worse by the fact that he knew this was going to happen and all he could do was leave a note before he die.This is the guy you have played as for over three games and he suddenly just passes away.Even Altair's death didn't compare to this.
The final sequence where Ezio discovers Altair's final resting place and the final Masyaf key. Manly tears were shed. "Just rest for a moment" indeed...
In 'The Last Archive' DLC, Clay's relationship with his dad. his dad's a total jerk to him, but Clay loves him throughout, even sending him an e-mail from inside the animus telling him it's not his fault that Clay died.
The E3 trailer (see above), though the extended version of the trailer (acting as the opening cutscene for Ezio's first Sequence) revealed that Ezio was not hanged at Masyaf and managed to escape.
- Seeing Ezio as an old man in Assassin's Creed: Embers. He's not old in the grey-bearded, still-as-agile-as-he-was-as-a-teenager way he is in Revelations, but in the longing for his youth, suffering chest pains and getting patted on the head in a slightly patronizing way by his daughter/wife way.
- The sneak peek of Assassin's Creed Embers. We see him leading a peaceful life and his strong and loving relationship with his playful daughter. But hearing his constant coughing and short breaths as he walks, let alone his pained breathing as he runs frantically towards his daughter after he sees and mistakes Shao Jun as an enemy, it really hits home just how little time he really does have left.
  - In the end, after a heavy bout of chest pains and coughing, Ezio's last moment is to look at his own smiling wife and daughter before he passes away on a bench in the Piazza della Signoria... where his father and brothers had been executed almost fifty years before.
- In an otherwise throwaway line between Sequences, Subject 16 causes a brief Heroic BSOD for Desmond when telling him not to be late for "Lucy's funeral!"
  - Compounded when Shaun mentioned that she had already been quietly buried in a little cemetery outside Rome, and when by Rebecca or Shaun that she did have feelings for Desmond.
- Altair's memories, where we find out that his late life was less than perfect. Especially...
  - The third one: While Altaïr had ventured east to deal with Genghis Khan, Altaïr's youngest son was wrongfully executed and told that his own father had ordered it. Altaïr came back to Masyaf only to be betrayed by his own brotherhood and lose Maria, when she put herself between him and one of Abbas' loyalists that Altaïr was using the Apple on, only for that loyalist to stab Maria in the back in his death throes.
    - It's even more heartbreaking if you've read the version of this event in The Secret Crusade: Someone close to Altaïr was wrongfully accused of the execution of Altaïr's son and when Altaïr confronts Abbas, he tosses him the head of that person -- Malik. Yes, THAT Malik.
  - The fourth one: Altair came back to Masyaf for revenge over two decades later, by which time the original Assassin was eighty-two years old, in a tattered brown robe and now only able to jog for a few meters before he involuntarily has to stop to cough...
  - The sixth and last one: Where the now-92-year-old Altaïr, having dispersed the Order around the world and given Niccolo Polo both the Codex and the memory-encoded keys in the fifth memory, shares one last goodbye and hug with his own aged son Darim before sealing himself and the Apple inside his library underneath Masyaf, essentially burying himself alive... and then the game forces you to walk Altaïr through his last moments.
    - Especially the bits of dialogue Altair hears as he walks through the library:

Maria: Get rid of that thing!
Altair: This is my duty, Maria!
Altair: (a few seconds later, sad and confused) Maria? Where... where are you? Where is she?!
Darim: Gone, father. You do not remember? She's gone!

- - - "Sit down and rest a moment..."
- Plus, in the fourth memory, as eighty-two year-old Altaïr makes his way to Abbas, you can see a glowing translucent figure sometimes around corners and in the crowds, but it vanishes before you can get close. It's Maria Thorpe. Altair has returned to the place where the woman he loves died, and he cannot. Stop. Seeing her. Everywhere.
  - Switch on eagle vision during those moments Altaïr will see flashbacks of his and hers visit 20 years prior. They are their last memories together still haunting him.