Near the beginning of the film, when Jason sees the bomb timer, you can see in his eyes that he knows at that moment he's going to die and there's nothing he can do about it. He just squares his shoulders and waits for the end to come.
The beating itself was just plain hard to watch, not helped by it being how the movie opened. Not many, especially those not on the up-to-date with Batman mythology, can watch a kid be beaten within an inch of his life like that without at least cringing.
Alfred's reaction to seeing that Red Hood's blood is a perfect match to Jason's is damn near heartbreaking. Especially since Bruce had never openly voiced his suspicions with anybody.
Ra's al Ghul's actions, despite having the best intentions. By hiring the Joker, he paved the way for Jason's murder, and by resurrecting Jason, Ra's inadvertantly drove him insane and set him loose upon Gotham. His remark as he orders his men not to pursue Batman sums up Ra's' feelings about the whole ugly mess.
Ra's: I have done enough.
The hopelessness of the moment when Jason just sits in a corner while a madman is choking his mentor and a bomb is ticking away to kill them all.
Two things make this scene all the more heartbreaking. One, when Batman does break out of Joker's grip, the first thing he does is actually reach out to grab Jason, totally ignoring the clown in favor of saving his surrogate son. Two, when the bomb goes off and reduces the building to rubble, Bruce begins to search through the rubble in the vain hope of finding what's left, if anything, of Jason.
Add a third thing: when Batman does grab Jason just before the bomb goes off, Jason has an obviously shocked look on his face, like he is surprised that Batman is bothering to save him at all...
Amazingly enough, the Joker gets one of these moments as well, in the same scene as the previous example. While the Joker is choking Batman he laughs hysterically, with tears in his eyes, that he's finally going to get his wish of dying with Batman.
Joker:(grabs Batman from defusing the bomb)NO! Don't spoil it! This is better! I'm the only one who's gonna to get what he wants tonight! Yes! Big bang boom! We all go out together! Don't you just love a happy ending? [laughs/cries hysterically]
In a flashback we see a pre-Joker wearing the 'classic' Red Hood costume, pleading with batman that it's not what it looks like and that he's 'not a crook'. He even tries to remove the helmet before tripping on his own cape and falling into the vats. For people who have read The Killing Joke, you can't help but feel sorry for the poor guy.
Batman admitting that he's always wanted to kill the Joker, but because he knows what thatwould meanfor him, will never bring himself to do so. Bruce's realSadistic Choice isn't the one offered by Jason, but the one he gives himself: spare the Joker, which would mean allowing him to continue his endless rampage and let Jason go unavenged, or kill the Joker, and lose his own soul in the process. Undoubtedly one of the greatest victories for the Joker, resulting in a complete Win-Win situation for him: Batman either kills him, and in doing so, completely loses his soul and lets the Joker die knowing that in the end he had the ultimate victory of forcing Batman to break his oath, or Batman doesn't kill him, and must instead live in sorrow/guilt for the rest of his life because the Joker has not only tainted the Robin legacy but successfully killed one of the few people Batman is close to.
"Why? I'm not talking about killing Penguin or Scarecrow or Dent. I'm talking about him. Just him. And doing it because... Because he took me away from you."
Nothing changed. The criminals killed by Red Hood will inevitably be replaced by more. Black Mask remains free, the Joker is back in Arkham, for all the good that ever does, and Jason, whether alive or dead, is still lost to Bruce, whose feelings of failure have, if anything, only gotten worse than ever.