The scene of Hometree being burned and brought to the ground. It's heartbreaking and terrifying at the same time, especially since it's inevitable that many Na'vi, including children, were killed.
The 9/11 parallels, said to be unintentional, are extremely eerie. From the collapsing tree trunks to the ash and smoke after the collapse, it really does resemble September 11th.
Colonel Quaritch stabbing the Thanator got a bit... violent. You can tell from the sadistic glee he has when twisting the knife into the Thanator's throat that he outright hates all things Pandoran.
And the fact that Neytiri, bonded with the Thanator at the time, felt all of its dying pain as her own.
Banshees and Thanators and Viperwolves...As beautiful as Pandora is, it's home to some terrifying lifeforms.
The earlier scripts had a bunch of much nastier creatures that never made it into the film proper, such as the Snake Tree, a Man-Eating Plant with six fanged heads like a hydra that baited it prey with half-eaten carcasses of its previous victims, the Slinth, a feline-like creature with a venomous harpoon for a head, or the Manticore, an earlier beta version of the Thanator that was equipped with a venomous stinger tail and scythe-like mantis forelimbs...
It's worse when you read the versions in the older scripts, where the constant predator attacks around the human settlement were not evidence of an over-hyped Death World. Rather, it was due to Eywa, the global hivemind formed by all living things, deciding that humanity's presence on the planet was an infection, and the beasts attacking the camp were its immune system trying to keep the infection contained.
When the Na'vi are shown losing the battle... that flaming direhorse...
What makes those few minutes when the Na'vi are being massacred indiscriminately even more horrifying & tearjerking is that things like this have actually happened in the real world. Not the mini mechas & the 10-foot-tall humanoids, but time & time again in our history indigenous people have gone up against a foreign power armed with vastly superior military technology in defense of their lands. Many of them fought bravely, sometimes extremely so. Yet, except for a handful of times, they lost. Very badly.
What happened to Norm's Avatar. What really makes it freaky is when he's forced out of his chamber, clutching his heart, shuddering and breathing...
A deleted scene reveals that Wainfleet walks up to him and shoots him at point blank range with that massive gun of his. Imagine the outcome of that...
Even if Norm's Avatar had a painless and pacific demise (which he hadn't, but that's beside the point), poor Norm actually experienced death. Not a near death thing, but for a moment he felt how it feels to die. Think about it.
So does Neytiri when her ikran Seze is shot.
Much of the final battle is this to the RDA troops who scream out in terror upon seeing their horrible imminent deaths, like the doorgunner who sees the other helicopter's rotors coming at him, or the soldier who falls when the Valkyrie is damaged and is crushed between two heavy pallets.
The soldiers on the ground when the Pandoran wildlife comes crashing down on them, literally in a few cases, and are crushed, gored or eaten alive.
Pandora's atmosphere is extremely toxic to humans, and yet it has just enough essential gases to make asphyxiation lengthy and quite painful - specifically hydrogen sulfide, which burns the mucous membranes lining the esophagus, and causes other nasty damage to the lungs. Even very limited and minor inhalation could result in permanent damage - luckily Jake tossed away his human body in the end. On average, a human asphyxiates from carbon dioxide build-up and poisoning while their head is trapped in a plastic bag from roughly 1 to 2 minutes. Due to Pandora's slightly lower C02 content (18%) and high enough presence of oxygen, it's stated that it takes roughly four minutes to fully suffocate. This is shown near the end where Jake is gasping for breath for quite some time before he collapses and starts convulsing, after his mobile lab was accidentally damaged and exposed to the air. If Neytiri hadn't shown up right then and there and quickly figured out how to operate the Exopack, he would've died a rather graphic and gruesome death.
This didn't make it into the final cut, but in the draft of the script, Tsu'tey survives his fall out of the Valkryie Bomber. Wainfleet, loaded up in his AMP suit comes across him. He doesn't shoot him. He doesn't stomp on him. Instead, he brings out a knife, picks up Tsu'tey by the queue and slices it off at the base. Keep in mind that a queue is akin to a Na'vi's nervous system. Tsu'tey's screams are said to be agonizing. Make matters worse, he holds it up like a trophy.
The scene where Neytiri tries to drag Jake's unconscious body through the forest while massive tree clearing machines roll towards them. Think about it: desperately trying to carry someone you just realized you love away from these machines that are so massive they are clearing away 20 ft tall trees like they were nothing. It's particularly heart wrenching to hear her screaming at Jake to wake up.
Not to mention that particular grove of trees was a direct link to her ancestors. RDA was essentially bulldozing a graveyard and cathedral at the same time.
In Avatar: Pandora Rising, in the background of the picture of the bio for Volodin, a Russian Mad Scientist who joined the RDA because he knew they wouldnt restrict his genetic/bioengineering experiments like the governments on earth did, an Avatar can be seen in a tank, that looks like the genetic material for a Viperwolf was added to the usual human/navi mix, while Volodin himself is about to cut into a dead viperwolf on a table in front of him.
His bio also mentions that the RDA is fully aware of his extreme and potentially deadly side projects, but the heads of the Transgenetics SciOps team look the other way because hes very useful. So, not only is Pandora a Death World with Everything Trying to Kill You, it is the current home of a Mad Scientist who wants to play Mix-and-Match Critters with its inhabitants.