When comparing WinSCP vs ssh of Cygwin, the Slant community recommends ssh of Cygwin for most people. In the question“What are the best SSH clients for Windows?” ssh of Cygwin is ranked 14th while WinSCP is ranked 17th. The most important reason people chose ssh of Cygwin is:
So you can have handy UI with tabs and other features. (For tab-like experience there is also GNU screen).
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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 May be used with console emulators like Cmder
So you can have handy UI with tabs and other features. (For tab-like experience there is also GNU 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.