WinSCP is a wonderful SFTP/FTP program that integrates very well with PuTTy. PuTTy and WinSCP are the “go to” tools for administrators and create a very easy to use workflow to get things done quickly. With WinSCP you can quickly drop to a command environment to issue a command via SSH.
Screenshots of the application:
WinSCP Configuration Screen
WinSCP gives a wonderful drag and drop interface to work with files including setting permissions and creating or editing files without having to download them or use a different application.