Tear Jerker / The Matrix Revolutions

• Sati meeting Agent Smith before he overwrites himself onto her. To reveal the truth to The Oracle, Agent Smith implies that he assimilated her by saying, "Cookies need love like everything does," which Sati said earlier. Although they left out the scene where she got assimilated, it's disheartening to witness this innocent little girl suffering the same fate that created the other Smith clones.
  Oracle: You are a bastard.
  Smith: You would know, Mom.
• The overall second half, with many beloved Zionites killed while fighting off the endless onslaught of sentinels, Neo and Smith's epic Final Battle in the Rain inside the Matrix and the beautiful Bittersweet Ending. It's all just one intense, emotional roller coaster.
• A small, but positive, heartwarming example: Trinity being the first human in centuries to have a brief glimpse of the Sun.
• Trinity's death, especially with her Final Speech and the Last Kiss she asks Neo to share with her ("Kiss me...once more...kiss me"). Never has Anyone Can Die been so painful.
• In a way, Smith becomes something of a pitiable character as the story wraps up, even as he remains a terrifying force of nature. His nihilism has driven him to an absolute extreme, to the point you get the impression he's trying to end all life so he can finally be done with it all.
  Smith: I really should thank you for it. After all, it was your life that taught me the purpose of all life: the purpose of life is to end.
• A Tears of Joy example; in the aftermath of the final fight, when the machines are retreating, and the Kid is rushing down into the caves of Zion loudly proclaiming "The War is Over!" at the top of his lungs. Sure, it cost them a savior (and to some, a personal friend) and countless lives, but Humanity had earned its victory.
  Morpheus: Is this real?
• Neo's Heroic Sacrifice in order to stop Smith's madness from destroying both the Matrix and the real world, and to finally bring peace between the humans and the machines. The last shot we see of him is his dead body being carried away by the machines, while music sad enough to make you cry by itself is being played in the background.

---