When comparing MobaXterm vs SSH of Windows' Linux subsystem, the Slant community recommends SSH of Windows' Linux subsystem for most people. In the question“What are the best SSH clients for Windows?” SSH of Windows' Linux subsystem is ranked 5th while MobaXterm is ranked 7th. The most important reason people chose SSH of Windows' Linux subsystem is:
All you have to do is go to the Microsoft store, choose a Linux distro you like, and install the client for free.
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Pros
Pro Flexible
MobaXterm can connect to practically anything.
Pro X server support
In case you need X11 forwarding, MobaXterm has an integrated X server.
Pro Full linux subsystem with package manager
And you can install conda for additional package management.
Pro Tabbed or split mode
Multiple terminals can either be in tabs or split horizontally or vertically.
Pro Integral remote file editor
Edit remote files via ssh and sftp
Pro SSH tunnel controls and forwarding UI controls makes it easy
Pro Automatic SFTP
With MobaXterm, there's no fiddling with multiple apps: simply connect and everything is available.
Pro Connection manager
Pro ENV can use Windows PATH
Pro Password vault
Pro Server tools (HTTPD, SSHD, SFTPD, TTFT)
Pro Build in sftp file manager
Manipulate and edit remote files in the file browser.
Pro Integrates with WSL
Integrates perfectly with the Windows Subsystem for Linux. Out of the box it offers a shell to that system.
Pro Supports macro controls (multi commands in single screen)
Pro It's extremely easy to get running
All you have to do is go to the Microsoft store, choose a Linux distro you like, and install the client for free.
Pro Based on OpenSSH
OpenSSH is the reference for all ssh clients.
Pro Excellent way for Windows users to learn Linux
It is much easier and more convenient than dealing with a dual boot Linux installation.
Pro Full Linux shell
Uses all relevant Linux ssh commands as normal.
Cons
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 Split screen prevents tabbed mode
If you split a screen within a tab, you have to go back to single screen before you can switch to another tab.
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.
Con Graphical problems
For example running Midnight commander (MC) makes terminal blinking.
Con Crontab and other background jobs don't work properly
Crontab only runs on ROOT, and it needs Windows to stay open. If you close it, you will kill the crontab. Some background jobs don't run on Windows WSL.
Con Command line editing does not work properly
Overrides chars instead of inserting them... depending on position and moon phase?
Con Does not install on PC virtual machines
Con Forces window to a certain size
Any other SSH client will render the remote server at whatever size the local client window is. The built-in SSH client on Windows, however, forces you to use a standard size, and it's small enough to cause problems.
Con Windows' SSH key agent service is broken
Attempting to use the built-in ssh-agent provided with Windows will cause errors and authentication failures due to an incompatibility between Windows' ssh-agent and OpenSSH on remote systems.
Con Cut & paste works like the Windows prompt
Older versions of the Windows Command Prompt select text in a rectangular region of the console, rather than starting at a character position and selecting forward or backward along with the logical flow of text. To copy a sentence, for example, would require that you select all content in the two lines that contain the sentence, then trim what isn't needed, rather than just selecting the sentence. In later versions of Windows 10, this may not be an issue, as the cut-and-paste behavior has changed.