Shallot is a file manager with the maximum degree of flexibility and customizability.
Unlimited number of file panels
Lots of customization options, e.g.
directory tree can be hidden and is flexible in behavior
lots of view options
while conserving a good usability
It nicely works with convoluted file systems, like editing an image in an archive in another archive on a network drive.
It has a plugin interface which allows one to implement many additional functionality (like new filesystems) with Python scripting, without any compiler hassles.