Mr. Freeze's reaction after Poison Ivy falsely informs him that Batman killed Freeze's wife is genuinely touching.
At the end, Batman tries to redeem Freeze (so he'll share the secrets of curing MacGregor's disease). And it works. And then they reveal that Batman actually saved Freeze's wife, rendering this plotline somewhat moot.
The conversation between Bruce and the ill Alfred, in what might have been their last moment together, and thus, tell each other what the other has meant to them in their lives. Say what you like about the rest of this movie, but the prospect of Alfred dying is genuinely sad, especially as played by master thespian and professional Cool Old Guy Michael Gough.
Bruce: I still have you, Alfred.
Alfred: I shan't be here forever.
The brief scene of Mr. Freeze carving a tiny sculpture of his wife into a makeshift music box is rather touching amidst the sound and fury and a nice reference to the animated series.