I think when Jake is walking up to the tree as Toruk Makto and his greeting with Neytiri.
You know they just want to fall into each other but they can't because of the situation. It's one of those wordless emotion scenes that gets me.
The other is after he wakes up and is walking through the ashes of the burned forest. He is so, so very dejected and guilt-ridden at what he caused.
Also when he's talking to Eywa at the tree, he knows how much loss there's going to be and desperately wants to try and cut their losses as much as possible. (Catholic symbolism moment there too, a Garden of Gethsemene scene... just realized that.) When he and Neytiri touch heads, they breath in each others breath.... wordless and beautiful.

Three scenes struck me the most;
1) when Jakesully becomes a member of the Omatikaya, as the the camera pans back and you see everyone (even Tsu'tey) lay on hands as a gesture of admittance and position
2) When Jake and Neytiri finally meet in their real forms, and despite being a Sky Person, she see and truly loves the soul that he is
3) When Jake comes landing in at the Tree of souls as Toruk Makto, where I could just hear him in my mind saying "I am the BADDEST Mo Fo on ALL Pandora"
That was cool

What Scenes hit me hardest!
 

1-The Seeds land on Jake as a sign from Eywah
2-Navi welcome Jake as part of the tribe
3-The Arrival/Speech of Toruk Makto
4-Swaying of Navi during prayer at Tree of Souls (helping Grace)
5-Riding to the four winds to gather the tribes

It didn't hit me as hard at first, but the last couple times I've watched the movie this part has seared right through me:

"You will never be one of The People!"

There are so many scenes that hit me hard, especially the scenes with epic backgound music like "Shutting down Grace's Lab" or "Destruction of Hometree".

But the scene which hit me always I watch the movie is the "I see You" scene at the end.
I can't explain why, but how she holds his human body and his hand on her face is so amazingly beautiful that I always cry.

"Jake, ma Jake..." :'(:(

I know exactly how you feel... :'(

One thing that caught me offguard tho was when the animals are all attacking the RDa troops, and the thanator turns to Neytiri and growls. I first thought that, "here she is, survivng a gun battle, only to be killed by the wildlife", not expecting it to INVITE HER TO RIDE HIM! Kaltxi palulukan!!:kiss:

When Jake is first brought to Hometree, & we see the Omaticaya clan. A civilization -young & older -familes, living & surviving on this plausible world (moon) of Pandora. It reminds me that one day us humans will find not just life & primitive life on exoplanets or the cosmos in general, but intelligent life that evolved & exist.

Oh, & other scenes roll with the rest of you-
* The fall of Hometree & the Omaticaya in shock & upset.
* "Eywa has heard you" scream from Neytiri, as the Ikran fly down from above.

1) Destruction of home tree
2) Scenes right after the destruction of Hometree
3) Tsu'tey's death scene
all 3 of these have almost gotten me to cry

jake and neytiri admitting their feelings for one another :D

That is a TOUGH question to answer. To be honest, the whole thing. Sorry that I can't give an individual scene or two. That's a hard question.

1. tsu'tey death scene made me cry, i still do
2. the "i see you" scene in the link chamber makes me sober
3. destruction of the hometree...

1. The destruction of Hometree. Seeing Neytiri lose her home, father and lover in less than a day and hearing her in so much pain :'(
2. Mating scene. The beauty of this is too much to bear and every time I see it, I wish I could be Jake.
3. The 'I See You' scene. After all they've gone through together they finally see each other and we know they are totally in love. You come away feeling warm and fuzzy knowing eveything is going to be ok :)

After the CE viewing, i'd have to say the scene between Grace and Jake about the school...

That really had me hurting inside. Although there wasn't a flashback bit or anything, there needed not be any pictures to accompany those words. :'(