When comparing PuTTY vs FileZilla, the Slant community recommends PuTTY for most people. In the question“What are the best SSH clients for Windows?” PuTTY is ranked 1st while FileZilla is ranked 10th.
Ranked in these QuestionsQuestion Ranking
Pro De facto standard client for SSH, Telnet and Rlogin
PuTTY is one of the oldest and most popular clients. It has earned the trust of a great number of users over a long period by being reliable, offering useful features and helpful support. It got into the 15 Essential Open Source Tools for Windows Admins list by InfoWorld.
Pro Source code available
Full source available. Compile and modify it yourself.
Pro Lightweight and portable
Pro Free and open source
FileZilla is free open-source software distributed under the terms of the GNU General Public License free of charge. Basically this means that everyone, including corporate entities, can use FileZilla, including but not limited to private, educational and commercial use.
In addition to Windows, FileZilla client is available for Unix, OSX and Linux.
Pro Suppots FTP and FTPS
FileZilla Server is a server that supports FTP and FTP over SSL/TLS which provides secure encrypted connections to the server.
Pro SFTP support
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 Lacks features
It is JUST an SSH client. There are many other options with built in X-servers, Multitabbing, etc.
Con Tedious logging/tracing
Its tedious to set up logging and tracing (e.g. for serial connections).
Con Ugly design, too simple
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 Installs junk software on your computer
The installer will install adware by default.