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 2nd while FileZilla is ranked 14th.
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
Doesn't require much resources (memory and hard-disk). Can even be run on a system by just downloading without install.
Pro Can be used on any Windows computer, even without admin rights
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.
Pro SFTP support
Supports FTP, FTPS (SSL) and SFTP (SSH)
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 Kind of de-facto standard
If you're troubleshooting things, everybody will first try if it works with File-Zilla.
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 Ugly design, too simple
Con Tedious logging/tracing
Its tedious to set up logging and tracing (e.g. for serial connections).
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.