Joey getting entangled by barbed wire. Seriously, without a doubt, it is the most powerful and incredible scene in the movie. Watching a panicked, terrified animal caught in the machinations of war bolt through trenches and explosions is War Is Hell personified.
Captain Nicholls' death was made quite heartbreaking with slow motion and the noise of the war being deadened.... not to mention his expression of knowing that he was going to die and being terrified of the certainty of it.
Hiddleston describes the direction he was given for the look on that face in that scene (in the film) as everything else peeled away and Nicholls being like a boy of nine again. It's not even fear, it's wide-eyed horror as he realizes exactly what's happened.
Emilie's grandfather giving away the last remnant of his granddaughter (Joey) to his original owner.
When the soldiers are basically looting Emilie's home and they take her grandfather's pot he uses to make jams. They almost take Emilie's medicines, too, but they settle for later taking Joey and Topthorn from her.
The German brothers being shot at dawn for desertion, especially after the eldest had tried so hard to protect his younger brother.
When Albert receives Nicholls' journal, out in the fields, and excitedly opens the letter to read it aloud in a glad voice. Within the first sentence is the news Nicholl has been killed in action, and the journal is full of drawings he was doing for him of Joey.
The scene in the play that takes place on Christmas, when Alfred is told that Nichols has died in the war. After his mother loses her temper and yells at him for only caring about Joey while half of the men in the village died with him, she apologizes and goes in to get something. Alfred then spontaneously decides to go over the Channel and look for Joey. His mother comes out and realizes what he's done, then runs back inside screaming for her husband.
Albert going over to the enemies' side and seeing all the bodies of the men he killed from a grenade he threw. He's horrified and full of remorse and it's clear he now knows why his father isn't proud of the things he did when he fought in the Boer War.
Major Stewart surrounded by German soldiers and forced to surrender after most of his troops have been slaughtered by machine guns. He drops his saber to the ground, with the harsh knowledge that not only is his cavalry dead the cavalry tradition itself has been rendered completely obsolete by modern technology.
In the play, Friedrich disguises himself and deserts the army, reporting himself as dead to continue the deception. He was driven to do this whilst knowing that it would cause massive heartbreak for his wife and daughter.