Batman & Superman: World's Finest - Karl Kesel et al.
Batman and Superman are the two most well-known superheroes (in the DC Comics universe, at least), and they are often shown together to contrast their different personalities and styles. (See, for instance, Kingdom Come or The Dark Knight Returns.) Superman is the Boy Scout, upstanding citizen in brightly-colored garb; Batman hides in the shadows, and fights crime with fear.
This particular story tracks Batman and Superman over the course of ten years: when they first meet, they spend too much time trying to outdo each other and an innocent man dies. They agree to meet once each year, learning to work together in an effort to attone for their mistakes. We get to see their relationship develop, from mutual suspicion to respect, to almost friendship.
But the genius of this particular tale is that it also manages to hit many of the highlights in each character's individual history, as well as showcasing a few of their villains (though Batman seems to have more than his share of those; Superman mostly just gets Lex Luthor). We learn about Robin, then Batgirl, and, later, Robin's death. We get a glimpse of the death of Superman and the arrival of the four new Supermen, as well as Batman's defeat by Bane and his new armor. Clark Kent finally marries Lois, and eventually reveals his secret identity to her.There's even a face-off between Mxyzptlk and Bat-mite, two very odd prankster characters. In the end, Batman and Superman both see that gleam of Metropolis hides darker crimes, and that even in the darkness of Gotham City light can be found.
Sure, it's just a comic book, and the deeper themes may be somewhat obscured by superhero cliches and bad plot devices like amnesia. But it's a good story nonetheless. And occasionally it demonstrates how there are some things you can do with comics that you just can't with prose: for instance, hiding graffiti in the background like the exhortation, "Read a real book!"