When comparing MobaXterm vs FreeFileSync, the Slant community recommends MobaXterm for most people. In the question“What are the best power user tools for Windows?” MobaXterm is ranked 27th while FreeFileSync is ranked 55th. The most important reason people chose MobaXterm is:
MobaXterm can connect to practically anything.
Specs
Ranked in these QuestionsQuestion Ranking
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 supports multiple protocols
It will work with MTP, FTP, SFTP, FTPS, and more.
Pro It can copy locked files
It supports Volume Shadow Copy Service, meaning that it can copy files even if they are in use or otherwise locked.
Pro Cross-platform
It runs on Windows, Linux and MacOS.
Pro Portable version available
Pro It is quite performant
Pro Google Drive support
FreeFileSync provides direct access to Google Drive, no additional software is needed.
Pro Completely free
Source code releases are provided under GPLv2.
Pro It supports realtime sync
It can be configured to constantly monitor two folders for changes and sync them instantly when a change is detected.
Pro It lets you program batch scripts
You can program your own jobs for execution as a script.
Pro It supports case sensitive synchronization
For Unix-like systems.
Pro It supports long file paths
It can copy files and folders with more than 260 characters in their paths.
Pro It supports versioning
Versioning is keeping multiple instances of the modifications of your files.
Pro It can sync both local disks and network shares
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 Does not preserve folder timestamps when copying
Con Memory hog
It runs a little slow on computers who don't have much RAM available.
Con Limited built in history
The program only remembers the latest set of folders you synced, so you have to save your syncs or create batch files.
Con A little intimidating for novices
If you never ran a file syncing software, this can be a little tricky to configure as your first one.
Con No backup encryption
Con It doesn't run on older Linux systems
It's dependencies don't allow it to run on older systems.
