When comparing WCM Commander vs Caja, the Slant community recommends Caja for most people. In the question“What are the best file managers for UNIX-like systems?” Caja is ranked 16th while WCM Commander is ranked 27th.
Ranked in these QuestionsQuestion Ranking
Pros
Pro Built-in terminal
Has a built-in terminal from which users can run any kind of command.
Pro Virtual file system
WCM Commander has a virtual file system for smb, ftp and sftp.
Pro Built-in editor
WCM Commander has a built-in text editor with syntax highlighting included.
Pro Easy to configure
Pro It has a reasonable set of features, out of the box
Not too much cluttered, but enough customizable.
Pro Caja script extension makes it more useful
Caja script extension adds your script in script menu, then passes the file name as a parameter. This allows you to run operation which is not included in Caja.
Pro Allows you to access remote or local locations
You can click the Files entry in the panel to access a specific location (remote or local), connect to a certain server (FTP, SFTP, SAMBA, etc.), access your bookmarks, open a new window, as well as to change its default functionality.
Pro Open or run as administrator in the right-click-menu of the mouse
Pro It just works
Customizable and clean, this is crushing that garbage nautilus, the overrated p.o.s. gnome destroyed.
Cons
Con File editing on virtual file systems not supported
You cannot edit files in the virtual file system.
Con Frequently very slow to transfer multiple small files
Folders move fine, but it chokes on files, where other browsers take seconds.
Con Mostly unconfigurable
There are not many ways to configure Caja to fit your needs. Besides what can be seen in the settings button you can't configure it further.
Con Sort Order / Limited Configuration Options
It ignores special characters when sorting files and folders. Underscore, tilde, bracket, ASCII characters, .... everthing not recognized in numeric/alpha sorting. Also, I found no way to remove the triangle to reveal contents of sub-folders rather than opening... but I did quit looking after several seemly unalterable functionality issues.
Con Very slow to list thousands of files
Unusably so.