Batman Run (21 issues +)
“52” #30 and #47
Batman and Son: #655-658
The Clown at Midnight: #663
Batman in Bethlehem: #666
Club of Heroes: #667-669
Resurrection of R’as al-Ghul: #670-671 (6 parts in other titles)
Three Ghosts of Batman: #672-675
Batman, R.I.P.: #676, DC Universe #0, #677-681
Lost in Time (32 issues+)
Last Rites: #682-683
Final Crisis #1-7 (especially #1, 2, 6)
Batman and Robin #1-9
Return of Bruce Wayne #1-5
Batman and Robin #10-15
Return of Bruce Wayne #6
Batman and Robin #16
Batman, Incorporated (24 issues)
Batman: The Return
Batman, Inc #1-8
Batman, Inc vol 2 #1-3, #0, #4-13
Here is my suggested reading order for the entire Grant Morrison Batman epic, 2006-2013. There's really no one right order, because when multiple series titles were telling the story at the same time, the publication order, the story logic, and the chronological time within the multiple series were mixed up three or four different ways. In at least two cases (the Arkham scene in DC Universe #0 and the respective order of the Batman and Robin and Return of Bruce Wayne finales), I think the publication schedule mixed up the intended logic. I think the transition from RIP to Final Crisis in particular makes more sense as I've offered it here, taking us through Bruce's experiences chronologically, instead of withholding the resolution to small mysteries for very long stretches of time.
Not mentioned here are the old stories that Morrison tied in, and the most important two were the Zur En Arrh story in Batman #113 and "Robin Dies at Dawn" in Batman #156. Others were reprinted in a trade paperback called The Black Casebook. However, while the small details of those stories were interesting reading while the Black Glove was an ongoing mystery, they aren't necessary to understanding Morrison's work. A rather large number of stories from 1939 through the Nineties are referenced by Morrison throughout his run, so the amount of background reading one could do would seriously add to the length of the list.
Finally, I'll make my best-of list-within-the-list. My favorite issues and scenes from the run.
1) Batman #680: Doctor Hurt's trap for Batman in Arkham.
2) Batman #674: Batman struggles to escape... and remember the past.
3) DC Universe #0: Batman and the Joker in Arkham.
4) Return of Bruce Wayne #6: Bruce ends the story of all time.
5) Batman and Robin #13: The Evil Thomas Wayne scene.
6) Batman #655: A replacement Batman shoots the Joker.
7) Batman #673: Batman's showdown with Joe Chill.
8) Batman #681: The RIP finale.
9) Batman and Robin #2: Frank Quitely draws Dick and Damian fighting the Circus of the Strange.
10) Batman #683: Batman escapes Darkseid's death trap.
If anyone reads this whole list in the order I suggested, I'd love to hear about it!