When comparing MobaXterm vs OpenSSH, the Slant community recommends OpenSSH for most people. In the question“What are the best SSH clients for Linux?” OpenSSH is ranked 1st while MobaXterm is ranked 2nd.
Ranked in these QuestionsQuestion Ranking
Pro Automatic SFTP
With MobaXterm, there's no fiddling with multiple apps: simply connect and everything is available.
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.
MobaXterm can connect to practically anything.
Pro Build in sftp file manager
Manipulate and edit remote files in the file browser.
Pro Full linux subsystem with package manager
And you can install conda for additional package management.
Pro Integrates with WSL
Integrates perfectly with the Windows Subsystem for Linux. Out of the box it offers a shell to that system.
Pro Integral remote file editor
Edit remote files via ssh and sftp
Pro SSH tunnel controls and forwarding UI controls makes it easy
Pro Connection manager
Pro ENV can use Windows PATH
Pro Server tools (HTTPD, SSHD, SFTPD, TTFT)
Pro Supports macro controls (multi commands in single screen)
Pro Password vault
Pro One of the most trustworthy development teams on the web
Pro The reference
If you find samples or tutorials about SSH, they almost always refer to OpenSSH.
Pro Standard implementation that documentation for all other tools assumes you have installed already
A lot of other tools (e.g. git) are based on this for file transfer.
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 Command line tool
It can be difficult to use from a command line interface.