When comparing Double Commander vs Caja, the Slant community recommends Double Commander for most people. In the question“What are the best file managers for UNIX-like systems?” Double Commander is ranked 4th while Caja is ranked 16th. The most important reason people chose Double Commander is:
You can use same tool in all desktop OS environments.
Specs
Ranked in these QuestionsQuestion Ranking
Pros
Pro Multi-platform (Linux, Windows, MacOS X)
You can use same tool in all desktop OS environments.
Pro Source code is available (true free software)
If the developer loses interest there is at least the possibility that someone else will pick up the torch.
Pro Configurable
Lots of options allow you to configure DC the way it suits you best: Tools, Fonts, Colors, Hotkeys, Mouse, Fileviews, Plugins, Layout, Toolbars, Tabs, Icons etc.
Pro Directory Hotlist
Save shortcuts to folders. Organize them in a treeview with submenus. Define a name and sorting for each entry.
Pro Powerful tcmd-like search tool (alt+F7)
Pro tcmd-like multi-rename tool (CTRL+M)
Pro DC uses TCmd plugin API
so you can use documentation from Total Commander for writing plugins. WCX (packer), WDX (content), WFX (file system), WLX (lister).
Pro Closely follows TotalCommander UX
For instance, the 'Settings | Layout' pane is quasi-identical to TCs.
Pro Very sophisticated
Although it is lightweight and simple to use, it can do very sophisticated tasks, like copying files from directories which have a certain extension or file size or have a certain text pattern in them. Also, it's very customizable and stable.
Pro It's that good, you can replace tcmd on windows too
Pro Source code written in (Object) PASCAL
It's all a matter of perspective. I'm not for an argument about IDE's, frameworks etc, but to me that's a big plus. I think it should be a tie, it's either a pro or a con or should that be neither a pro nor a con. It just depends on context.
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 Apparently only one developer
Con Freeze after mouse double-click on directory list item
Con Much slower on Linux and Mac than on Windows
Con Source code written in Pascal language
But this does not affect users negatively. It's just programmers problem.
Con Not developed anymore for Mac
Con Can't edit files on remote FTP servers
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.
