No way i'll ever be able to pick a single issue, but here's my current top five (i.e, the issues i go back and re-read on a regular basis);
Batman #260 - "This One'll KILL you, Batman" by Denny O'Neil...One of my favorites since childhood. Mainly because we get to see a demonstration of Batman's many fighting skills during one brutal battle. Two-Face has tipped Bats off that there is about to be an escape attempt from the mental ward (dont think Arkham existed yet, have to dig it out later and check), and Batman gets there just as about two dozen inmates are about to escape. Bats utilizes several different martial arts disciplines while attempting to subdue them....besides all that, this is also a pretty cool Joker story as well. Joker has poisoned Batman, and Bats has 72 hours (iirc) to locate the couple doctors with the ability to save him....Joker, of course, is on his way to murder them first.
Detective Comics #454 - Another great issue featuring The Dark Knight's many fighting skills. Wanted felon, and all around bad apple Rex Giles has decided to take Gotham's Guardian down a peg or two. He hires several different "ultimate fighter" types (each disguised as Giles himself), to pick a public fight with Batman. The point being, to figure out Batman's fighting style and come up with a way to defeat and humiliate Batman in front of a crowd. We also get to witness Batman's
excellent analytical skills, as going over each fight in his mind, he realizes Giles is setting him up for a major beat down. When the two finally meet on the mean streets of Gotham, Batman proves once and for all that the city isnt big enough for both of them!
Detective Comics #455 - "Heart of a Vampire", by Elliot S Maggin...I try to dig this one up each Halloween. Returning from a road trip, Bruce and Alfred's limo breaks down on the outskirts of Gotham...right in front of an old, decrepit mansion...turns out to be the home of Count Gustav DeCobra, vampire lord! Shouldnt be a problem for Batman, right? Simple stake through the heart and call it a night? WRONG! The evil count has had his heart removed to an undisclosed location in the mansion, and Batman better find it quick before he and Alfred end up as a midnight snack. Very creepy issue!
Killing Joke - Alan Moore. Great issue...this was really the first time i remember seeing Joker's past and motivations explored with such great detail...when this book came out, it was the topic of conversation at the comic shops for the next several YEARS. Great debate on whether or not Joker sexually assaulted Babs after crippling her...best part of all though, was seeing Batman offer Joker a chance at redemption....and Joker, for a split second, nearly accepts! To me, this remains one of the best Batman stories, and certainly THE best Joker story, ever.
Batman Annual #19 - Nothing particularly earth shattering here, other than like Killing Joke, we get to see the background of another great villain explored, this time being Scarecrow. I just dig him, what else can i say?
Would've said it sooner but, ironically, I can never seem to remember the ish #. 
