When comparing cmder vs MobaXterm, the Slant community recommends cmder for most people. In the question“What are the best terminal emulators for Windows?” cmder is ranked 2nd while MobaXterm is ranked 4th. The most important reason people chose cmder is:
Cmder builds on [ConEmu](https://code.google.com/p/conemu-maximus5) console emulator, by adding enhancements from [clink](http://mridgers.github.io/clink/) (such as bash-style completion in cmd.exe and PowerTab in powershell.exe) and optionally extending it with [msysgit](http://msysgit.github.io), that brings Unix tools to Windows.
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Pro Minimal and portable version available
There is a portable version of cmder available which is just 10 MB in size. It can be put on an external device, like a USB stick, and run off it. There's no installation required.
Pro Monokai color scheme
Cmder pretties up the default look of ConEmu using Monokai color scheme out of the box and allows flexible color and transparency schemes, including custom out-of-focus opacity.
Pro File explorer integration
Cmder can be added to the right-click menu, allowing the user to start a terminal session from the selected directory with a "Cmder Here" command. The functionality can be enabled by opening up a terminal with administrator privileges, navigating to the Cmder folder and executing
.\cmder.exe /REGISTER ALL.
Pro Works nicely with command line applications
Such applications include CMD, Powershell, and MinTTY.
Pro Has built-in Quake style drop-down mode
This is an extremely useful mode whereby the console hides and shows on ctrl+~ similarly to a gaming console.
This feature is inherited from ConEmu.
Pro Integrates with graphical applications
Portable GUI applications can be integrated directly into the interface of the terminal emulator.
For example, it's possible to integrate ST3 with cmder by moving the portable version of ST3 to
/cmder/vendor/ and editing alias file in
/cmder/config/aliases to include
subl="%CMDER_ROOT%\vendor\Sublime Text 3\sublime_text.exe" $1 -new_console:s75V. Now writing
subl in the command line will open ST3. The alias of subl can be changed to whatever's needed and similarly, the
-new_console option's parameters can be changed to alter how the text editor integrates with the terminal emulator. It can be horizontal or vertical splits of varying sizes or tabs, etc.
Pro Highly flexible
Pro Automatic SFTP
With MobaXterm, there's no fiddling with multiple apps: simply connect and everything is available.
Pro Full linux subsystem with package manager
And you can install conda for additional package management.
MobaXterm can connect to practically anything.
Pro X server support
In case you need X11 forwarding, MobaXterm has an integrated X server.
Pro Tabbed or split mode
Multiple terminals can either be in tabs or split horizontally or vertically.
Pro Build in sftp file manager
Manipulate and edit remote files in the file browser.
Pro Integral remote file editor
Edit remote files via ssh and sftp
Pro Integrates with WSL
Integrates perfectly with the Windows Subsystem for Linux. Out of the box it offers a shell to that system.
Con Issues with non-unicode characters
'ls' command can have issues with non-unicode characters such as cyrillic. As of 1.1.2, 'dir' can be used as a substitute that will properly display non-unicode characters. Unfortunately, it's an issue with msysgit that isn't being officially addressed (a workaround is available) thus no official ETA on the bugfix is available.
Con very very slow
Con Not as portable as advertised
Even though cmder is advertised as a "portable terminal emulator for Windows", it's not adequately minimalistic to be considered truly portable. In fact, one of the dependencies required to use it is the Visual C++ Redistributable for Visual Studio 2015.
Con Slower than ConEmu
Con The portable (mini) version does not have UNIX commands
UNIX command support is only available for the full version.
Con Not completely freeware
If you use MobaXterm at work, they hope you will pay for it. This isn't horrifying, but it's not providing any new features in Linux to warrant the outlay. Its integration with Putty in Windows as an X client may make it worth the funds.
Con Can have some performance issues
MobaXterm can have some occasional performance issues. These happen rarely but it's worth mentioning that they exist, especially since this is a paid tool.