The "No Way Out" scene where Kenai has to tell Koda that he killed his mother.
Kenai: Koda, I did something very wrong.
Koda: I don't like this story.
Kenai: Your mother isn't coming.
Koda responds with a Little "No" before he darts off in disbelief, climbing a tree and watching Kenai dissolve into a Heroic BSOD.
The original version of this scene skips the song, allowing us to hear Kenai's story from start to finish. The way his voice steadily cracks, all the while Koda is slowly putting the pieces together...it's utterly gutwrenching.
And, if it were possible, the dialogue is actually worse than the final version of the scene.
The way Koda is so cheerful and affectionate with Kenai, and Kenai averts his gaze, rebuffs Koda's hug, and sets him aside, in a you're-giving-me-way-too-much-credit sort of way.
As the three brothers are reuniting on the mountain, Koda is communing with the spirit of his deceased mother, a final farewell before she joins the Spirit Plains forever. One can only imagine what they're saying, but you can bet it's a tearjerker.
The moment just a few scenes later between Rut and Tuke over what it meant to be a brother, right in front of Koda, who realizes despite the mistakes his brother made, he saved him several times, showing that he did love him and that he could change, just like the moose brothers.
What about the scene where Kenai is forced to fight his brother to try and protect Koda and they're trying to kill each other and they're brothers...? That really gets me...
The shocked and sad look on Koda's face in the sequel after Kenai yells at him to stop scaring Nita with the salmon. Yes, Koda was going a little overboard, but the sad look on his face...aww.
Sitka's funeral. All Kenai and Denahi could find of their brother was the torn piece of his parka and his eagle totem and it's burned right in front of them. The only things they have left of their big brother is burnt to ashes in front of their eyes and now they're both all alone in the world. It's Tanana's line straight after which really seals it.
"You left too soon, Sitka. Your brothers need your guidance."
In the sequel, Kenai hides Koda to try and draw away a hunter. You can see the horror on Koda's face because that's probably exactly the last thing he remembers his mom doing before she died fighting Kenai.
The disappointed and almost remorseful look on Sitka's face when he appears to Kenai moments before the latter is transformed into a bear. Especially since Kenai just killed the bear he thought was responsible for Sitka's death.
Especially worse is when Denahi arrives on the scene just moments after Kenai's transformation and sees Kenai's torn clothing and believes his own little brother is dead.
For that matter, the look on Sitka's face right before he breaks the glacier and plunges both himself and the bear into the lake below. The bear survives. He doesn't.