For me it was Frank Miller's "Born Again" story with Daredevil. I prefaced it by reading his earlier run on the character - which I thought was pretty solid, if a little dated.
Overall I found "Born Again" to be rather 'meh.' I don't see how it's one of the greatest comic book stories of all time - or even the greatest DD story for that matter. I did enjoy the first third of the story arc, but it seemed to deteriorate into a random mess, and finally the emergence of Nuke felt bizarre and off-point. I also didn't like how Captain America slapped a lowly soldier for following orders - what a douche. I've liked other works by Frank Miller, so it really surprised me that I wasn't a fan of this.
So what "great" comic book story didn't work for you?