Gordon's confrontation with Flass in Batman #404 is probably my favourite Gordon moment of all-time. Those final two panels on page 18 almost give me goosebumps whenever I read them. You know that Gordon is a badass, but you don't get to see that in action in very many books, at least that I've read, and that line, "Even so -- he deserves a handicap", is great stuff.
I feel like I haven't read enough Batman stories that deal with Gotham in a way Year One does. As you said, Scarlet, this is a Gotham that exists before the super-villains take the spotlight from the organized crime, but there's something about the dark, gritty, stories that show the awful sides of Gotham that I really enjoy, and that's one of the reasons I like this story as much as I do.
I'll make note of it and make sure we get to some other "organized crime is the scourge of Gotham" stories sooner rather than later. ---
"It is too easy being monsters. Let us try to be human." ~Victor Frankenstein, Penny Dreadful