I'll do a top ten of best movies by director duos. What I won't do is include any movies that were half-directed, then picked up by someone else. Those are mostly shit, anyway.
As per usual, I won't repeat duos, so it won't be a top ten Coen Brothers list.
Top Ten Movies With Two Directors
10) Delicatessen (1991) Marc Caro & Jean-Pierre Jeunet. The best of their collaborations, Jeunet went on to make his own mark with Amelie.
9) Sin City (2005) Frank Miller & Robert Rodriguez. Though the long-awaited sequel soured our hindsight, this movie was tremendously well-received and nearly revolutionary in convincing studios of the potential of comic properties.
8) Airplane! (1980) David & Jerry Zucker (and Jim Abrahams?). I guess this had three directors? Still, the best Zuckers film, save for a personal nod to Top Secret.
7) Little Miss Sunshine (2006) Jonathon Dayton & Valerie Faris. This didn't play for everyone, but it did for me. And for the Academy.
6) About a Boy (2002) Chris & Paul Weitz. The best Nick Hornby adaptation?
5) American Splendor (2003) Shari Springer Bergman & Robert Pulcini. Giamatti unleashed onto the world! A great comics property (thanks Harvey Pekar) and a wonderful film.
4) Dumb and Dumber (1994) Peter & Bobby Farrelly. Some might say There's Something About Mary is their best. I don't.
3) Captain America: The Winter Soldier (2014) Joe & Anthony Russo. Best comic book movie ever?
2) The Matrix (1999) The Wachowskis. No need to explain.
1) Fargo (1996) The Coen Brothers. Lotsa different opinion on the Coen's best film. I'm a huge fan of most of their work, but to me, Fargo is the smoothest and most accessible.
Short Answer: Honorable Mentions: Can't Hardly Wait, Bad Santa, King Kong, Half Nelson, every other Coen Brothers' movie.