In the censored version of the events leading to Jokers death, Tim immediately tosses the gun given to him by Joker to kill Batman aside, causing Bruce to smile with pride.
Moments later he jumps the Joker freeing Batman from Joker's grasp.
In the uncensored version, he shoots the Joker instead when he orders him to murder Batman. He then slowly returns back to his senses.
The ending scene at the hospital, where the Bat-Family are together again after nearly 40 years apart.
Bruce gives Terry this advice before entering the hospital room:
Bruce: Terry... I've been thinking of something you once told me. And you were wrong. It's not Batman that makes you worthwhile. It's the other way around. Never tell yourself anything different.
Right after that, Bruce and Tim talk to each other for the first time in almost half a century:
Bruce: Hello, Tim.
Tim: Hi, old man.
It should be noted that the "old man" part was not sarcastic at all... which makes it even more heartwarming.
Subtly, bear in mind that the Joker really did die, and Harley was childless at the time. She moved on.
Not only that, but she really is pissed that her granddaughters were engaging in criminal activities. Not only did she move on, but she broke out of her own criminal mindset and wanted her family to be on the straight and narrow.
A blink and you miss it one from the flashback, but Harley actually seems to try and protect JJ (brainwashed Tim) at one point. Perhaps the desire for children was more genuine on her part?
After being attacked by the resurrected Joker and his gang, Ace recovers by watching classic WB cartoons.
And Terry makes it a point to check up on him.
When Terry visits Tim in the hospital after the crisis is over.
Tim: For what it's worth, Bruce couldn't have chosen anyone better to put on the mask.