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Several, most notably the destruction of Hometree, Grace's death, and Neytiri's father's death.
The Hometree destruction was especially tearjerking for this fact: Ever see hundreds of people break down crying before? No?
Also when Trudy's gunship was shot down, when Neytiri saved Jake from suffocating, and when Jake permanently enters his Avatar body at the end.
When Jake is formally adopted into the Omaticaya, we see Grace looking on, doing her damndest not to cry.
Tsu'tey's death, especially in the extended cut. "He was my last shadow."
The Na'vi school in the extended cut. We first see it being used as storage after being abandoned, and after Jake sees some bullet holes in a blackboard and asks Grace, she snappily changes the subject. Later on, after Jake and Grace have grown closer, she tells him exactly what happened. Sylwanin (Neytiri's sister) and a group of young hunters attacked an RDA bulldozer and ran to the school, thinking Grace could protect them. When the troopers arrived, they not only killed Sylwanin right in front of Neytiri, but also many of the students. Grace's "I got most of the children out" line really drives it home.
The opening shot
Neytiri holding human Jake
The entire scene at the Tree of Voices
Jake's first flight
Selfridge finally realizing that he made a mistake while watching the destruction of Hometree. But it's too late.
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