I am frankly a little shocked that "Knightfall" has only been mentioned once here. Moreover, that it was only brought up as a being highlighted by many villains. Knightfall up until Knightsend is kind of the last hurrah of the more human Batman of the 70's and 80's, and for my money it's the quintessential Batman story (not that the post-Knightsaga superBat is without his own appeal, and no offense to Frank Miller: they just can't touch this). This is the definitive story about Batman's will, his drive, and while we are not treated to the painful repetition of the Waynes' murders that has become so formulaic in describing Batman's motivations, Knightfall puts most other storylines to shame.
The Knighfall storyline pushes Batman to his limits, and is from beginning to end a story about how he takes on incredible odds, placing superhuman burdens upon himself. By the halfway mark Batman's already holding on only through the sheer force of his will. This is what appeals about Batman: that he holds himself to an unachievable standard, and that he pushes himself beyond human endurance. Of course in the end of this story he fails, but that only really drives the point home. The comeback of Bruce Wayne in Knightsend is a fantastic story as well: he tries to regain his edge, experiencing some of that self doubt that the character has been more or less devoid of in more recent stories. I really like his frequent returns to the tower (I want to call it Wayne Tower, but I'm not sure if he's bought it yet by this point in the series), where Bruce tries to summon the will to leap off as he did when he was Batman, without hesitation. Just top notch stuff all around: the only real problems are that if you're not familiar with some of the backstory going in some aspects of the story (most notably Jean Paul Valley) might throw the reader off a little bit, and that the "Knightquest" section of the story is not available in one convenient collection, so you'd have to track down all the individual issues to read it (but that's not a big deal, Knightfall and Knightsend stand on their own just fine). These are stories that represent Batman as he is best understood: a mortal man with limitations, who nonetheless pushes himself towards the impossible goal he set for himself. It also demonstrates that because he is only a man, even the best and most capable of men, he is bound to experience failures and doubts. What he is not is a relentless and unerring vigilante-machine, as some stories regrettably represent him as.
I found that the two throwback storylines "Batman and the Monster Men" and "Batman and the Mad Monk" did a good job of representing Batman in a similar light of a man with limitations and doubts, and in this rare case, hopes... hopes which are disappointed, of course. "Batman and the Monster Men" also has a pretty compelling representation of Hugo Strange as the villain, and both storylines feature Jim Gordon dealing with his relationship to Batman in one way or another.
Now, some may disagree vocally with this last bit, because of the awesome asskicking robot Batman that the next selection displays, but I really liked Jeph Loeb's work on Superman/Batman. In particular the first storyline, Public Enemies. Now, on the one hand, I appreciate that the vast number of villains and heroes that the Worlds Finest duo trounce and the ridiculous amount of chaos they routinely deal with in the Superman/Batman series can be seen as nothing more than fan service displaying how awesome the title characters are. On the other hand, that's just part of the fun of having the two greatest superheroes in the world starring in the same comic, and it's not really the part I find most appealing. What's at the heart of the storytelling in Superman/Batman, especially Public Enemies, is the dual narration by Batman and Superman. While at times they're taking opposite positions, Superman the optimistic and Batman the pessimistic, when push comes to shove we see they're basically coming from the same place, that they have profound mutual respect and friendship, and that more often then not they come to similar ends, though through slightly different means. I find the whole ride delightful, it's one of my favourites.