I use cwrsync on the Windows machines, running as SYSTEM and pushing their files to a Linux rsync server. It uses a password in a plain text file to authenticate with the rsync server
cwrsync can also use ssh but I am not familiar with it.
Amanda is similar in that it uses CIFS (were SMB) shares to get the Windows files and so uses Windows users' passwords.
A better solution might be to use Bacula which can be run as a service on the Windows systems so does not need to use CIFS. Bacula has its own client/server passwords.