Amazonia is another one I thought was really well done.
Favorite books right now: All-Star Batman, Wonder Woman, Moonshine, Groo, Usagi Yojimbo, Cave Carson has a Cybernetic Eye and a Too Long Book Title
Also good readings: Titans, Midnighter and Apollo, The Autumnlands. Great Lakes Avengers
I personally liked all of The Kingdom, but I'm weird like that.
JSA: Liberty Files is excellent
Batman: Thrillkiller features Barbara Gordon in the driver's seat. Haven't read it in a while, but I remember enjoying it.
Batman: Detective 27 is almost like League of Extraordinary Gentlemen with American historical figures
Honorable mention: Squadron Supreme by Mark Gruenwald, which is as "hardcore" of a Justice League story as you can get (other than The Authority)
Most of my favorites (Golden Age, Jla: The Nail/ Another Nail, Kingdom Come, Superboy's Legion, etc) have been mentioned, but Superman Kal with art by Jose Luis Garcia Lopez is an underrated gem.