Great list Milk Tray. But I would expect nothing less from you. I too love Throne of Atlantis and the ending left me beyond sympathetic toward Orm. I really felt for the guy.
I’m sure my list is probably controversial or maybe just weird in places, but here goes:
1. Kingdom Come - for me, THE definitive graphic novel.
2. Superman, Up Up & Away - I hadn’t read this until the last few weeks but I did after hearing guys on these forums gushing over it. It has vaulted over All Star and Birthright for my favorite Supes story.
3. Battle for the Cowl - a guilty pleasure for sure. I love this story. Nightwing is a boss. He’s more than a boss in this story. He’s the boss of all bosses
4. Forever Evil - I’m a sucker for this story. But it has to be read in conjunction with the tie in involving The Rogues
5. Knightfall - it lags with Azbats but it is just so epic and takes its time. I like to read Batman Prodigal as an epilogue.
Honorable mention: it is so close but I almost included No Mans Land. I absolutely adore that entire run. Words can’t describe how much I love many of the individual stories, most notably the ones involving Helena, Scarecrow, Ivy and Cassandra. I think the lack of a consistent artist threw me off. If you ever want a succinct showcase of human nature and to see the difference in how Superman and Batman perceive the world, check out when Supes shows up (briefly) in the story. I almost put it above Knightfall
I would also add Throne of Atlantis to my honorable mention. I love Aquaman. Absolutely love the character and he is on full display here. I think my only drawback is how this story seems to be the only story that writers can come up for the character. It has been repackaged over and over in other stories. But this is the best iteration.