Comment 5 for bug 1244371

The following is the recommended way to manage permalinks:

 location / {
    try_files $uri $uri/ /index.php?$args;
  }

Source:
http://codex.wordpress.org/Nginx

The page says "This was fixed in WordPress 3.7, which now detects nginx servers and enables "pretty" permalinks automatically. " Maybe there is even a way to do this automatically then?