The Confederate outpost Angel Eyes encounters in the extended cut of the movie. The terrible conditions the soldiers were left in were enough to have him feel sympathy for them, even as he's doing his job in looking for Bill Carson.
The scene where Rebel prisoners are forced to sing loudly to drown out the sounds of Wallace beating the crap out of Tuco. Many of the prisoners are visibly weeping, as they know exactly what's happening to Tuco inside the cabin, but they can't do anything to help the poor bastard. The lyrics to the song "Story Of A Soldier" make it even sadder:
Bugles are calling from prairie to shore, "Sign up" and "Fall In" and march off to war. Blue grass and cotton, burnt and forgotten All hope seems gone so soldier march on to die.
Bugles are calling from prairie to shore, "Sign up" and "Fall In" and march off to war. There in the distance a flag I can see, Scorched and in ribbons but whose can it be How ends the story, whose is the glory Ask if we dare, our comrades out there who sleep.
The scene where Blondie comforts the dying soldier and leaves him his jacket.
Tuco trying to find the grave where the money is buried. He runs through the vast graveyard, trying to find one particular tombstone in a forest of tombstones to fallen soldiers slaughtered in a tragic war, as Ennio Morricone's "The Ecstasy Of Gold" works up towards a climax.
Captain Clinton deserves a spot here. After getting fatally wounded in battle, through sheer force of will, he stays alive long enough to watch Blondie and Tuco blow up the Branstone Bridge he's been bitching about. When it happens he dies with a smile on his face.
Captain Clinton: Can you help me live a little more? I expect good news.