Like I said, the whole Knightfall/Quest/End had a lot of filler, but, overall, the story works. It just should've been about a quarter of the length. Bane finally busting in on the Batcave and literally just beating the shit out of Batman for a full issue redeems the filler.
Year One and Shaman are tied really closely together. Gothic as well, but not as closely.
Year Two sort of stands alone. There was a return of the Reaper story, but it wasn't up to the original. (Zero, I think they should scrap Reaper, and bring the fucking Phantasm into regular continuity. Retcon her into his origin somehow. She kicks ass.)
A Death in the Family, Year Three, and A Lonely Place of Dying must be read in that order, or they won't make sense.
No Man's Land was a grand experiment, and one of the very few on that scale that worked. After the silliness leading up to it, Gotham is a wasteland ruled by rival supercriminals. Bruce Wayne has been in Washington speaking against Nicholas Scratch (again, who's never fully given a motivation for this craziness), so Batman's been gone. Gordon is leading the resistance, but no longer trusts Bats because of his absence. It's quite good.
The Killing Joke may actually be the best Batman story ever told. It's certainly the best Joker story ever told. It's coming back in an anniversary edition, but it may still be cheaper to get either an older edition or the collection of DCU stories by Alan Moore.
