Ra's al Ghul saying "I've done enough" as Batman leaves. Considering this is Ra's al Ghul we're talking about, this is actually rather touchingnote considering that his regret is that he indirectly got Jason Todd killed and his attempt to make up to Batman for it instead resulted in Jason Todd as the Red Hood.
Followed shortly by this darkly heartwarming gem that proves Jason still loves Bruce in his own way: "If it had been you that he had beat to a bloody pulp, if he had taken you from this world, I would have done nothing but search the planet for this pathetic pile of evil, death-worshipping garbage... and sent him off to hell!"
Batman thanking Nightwing for his help.
Really the relationship between the two. Dick may not have been in the movie for very long, but during his screentime, there wasn't any tension between him and Bruce. This might imply that they either never had the fight that made Dick leave, and he became Nightwing just because he was getting too old for the Robin thing, or they did have the fight, but they've moved past it.
Jason pointing out that Two-Face, the Scarecrow, and the Penguin have a chance at redemption. If you remember, Two-Face killed Jason's father, and yet he'd sooner forgive him than the Joker.
When Red Hood and Batman team up to take on the Fearsome Hand of Five, Hood takes a bullet for Batman. Even if Jason is furious with Bruce, and may never forgive him for not killing Joker to avenge his death, he still cares about the man who he sees as a father.