When comparing WinSCP vs MobaXterm, the Slant community recommends MobaXterm for most people. In the question“What are the best SSH clients for Windows?” MobaXterm is ranked 7th while WinSCP is ranked 17th. The most important reason people chose MobaXterm is:
MobaXterm can connect to practically anything.
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Pros
Pro Supports FTP and SFTP
In new versions also supports WebDav.
Pro Free and open-source
It has very good compatibility with the other tools of this segment (e.g. PuTTY).
Pro Supports WebDAV
Pro Not bundled with Potentially Unwanted Programs (PUP)
Does not attempt to install unwanted software on installation.
Pro Supports PPK Keys
You can use the SSH server public/private key files from putty to log in.
Pro Supports Amazon S3
You can use in the last versions S3 so you're good if you use Amazon AWS.
Pro Portable
No Installation required.
Pro Integrated basic text editor
It has a integrated basic function text editor to create/edit/update files directly from client.
Pro Can protect stored passwords by strong AES cipher
Pro Can be automated with batch scripts
Put a line in bat file ""D:\Program Files\WinSCP\winscp.com" /console /script="D:\ftp\scripts\transfer.txt". All the info can be found on their site.
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)
Cons
Con Keyboard shortcuts not editable
Con Slow
In my opinion, it's slower than Filezilla.
Con No x64 version
Con Does not support UNC
Does not support UNC. This makes working with the "Library"-function in Win 7, 8, 10 not possible when working over a network.
Con Weird keyboard selection handling
If you are accustomed to several commanders, the selection method in WinSCP behaves unexpected - most often selects too much.
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.