This hasn't been mentioned at all, but I'm going to say the majority of Batman books flourished in the 90s when DC, Marvel, and so many up and coming Comic labels were in the stink hole!
First of all, you had Batman regularly mourning Jason Todd, which furthered his crusade at times. There was the development of Tim as a character to take serious and care about. You had the lead up to Knightfall, which was exceptionally brooding and bold. Then there was Knightfall itself, which is a flawed masterpiece. Following KF was the often unnoticed Batman: Contagion storyline, which lead to Legacy, the precurser to Cataclysm & No Man's Land. And I know NML wasn't the fondest of Bat-stories, but it was big & dangerous & allowed the supporting Bat characters to flesh out even more.
...Not to mention all of Loeb's work w/Tim Sale.
I'd say Batman (and related books) was the best overall superhero book of the 90s, not counting mature reads from Vertigo.