When comparing PuTTY vs WinSCP, the Slant community recommends PuTTY for most people. In the question“What are the best SSH clients for Windows?” PuTTY is ranked 1st while WinSCP is ranked 10th.
Ranked in these QuestionsQuestion Ranking
Pro De facto standard client for SSH, Telnet and Rlogin
Pro Source code available
Full source available. Compile and modify it yourself.
Pro Not bundled with Potentially Unwanted Programs (PUP)
Does not attempt to install unwanted software on installation.
Pro Free and open-source
It has very good compatibility with the other tools of this segment (e.g. PuTTY)
Pro Supports FTP and SFTP
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
Con Tedious logging/tracing
Its tedious to set up logging and tracing (e.g. for serial connections).
Con Lacks features
It is JUST an SSH client. There are many other options with built in X-servers, Multitabbing etc.
Con Can not save passwords
Anyway, you can use "PuTTYgen" to generate a key pair, then use "Pageant" to do a password-less SSH remote login.
Con No global settings
If you want to change a setting for all your connections, you'd have to do it individually.
Con No login scripting
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.