"Superman [and] Batman: Public Enemies" by Jeph Loeb and Ed McGuinness
This limited series was recently adapted into an animated feature which I have yet to see. Say what you like about Warner Bros. strategy for creating a "DC Cinematic Universe" - the fact remains that they've been working overtime when it comes to cartoons. I saw the "Flashpoint Paradox" cartoon not long ago, and I was surprised by its level of quality.
In "Public Enemies," Superman and Batman team up to foil a plan by President Lex Luthor. Jeph Loeb tries very hard to draw parallels between the two heroes, and to provide situations in which their abilities compliment one another. Loeb certainly shows a lot of versatility as a comic book writer, and what one sees in "Public Enemies" is VERY different from Loeb's work on "Red Hulk" or "The Long Halloween."
I'm not a huge fan of Ed McGuinness's art. He is obviously very competent, but I can't help but compare him to Tim Sale, who drew the introductory chapter to this series. I realize that comparing Sale and McGuinness is like comparing apples to oranges, but I can't help but think that McGuinness sacrifices style for the sake of technique, where Sale is all about style. In the long run, I think, style wins.
I'm also wondering if Zack Snyder has read this comic. Given that "Batman Vs. Superman" is now (officially) in the works, series such as this one might well provide a template for any script based on the two characters. The Justice League and supervillains could easily be excised from the plot, and what you'd be left with is a solid drama about two heroes learning to work together as a duo. This, in turn, would set up the future "Justice League" quite nicely.