SyncBack (the freeware versoin, not the "I cost money" version) is a good utility that I use at work. It will allow you to setup directories. You can zip each directory, or whatever selection of directories you are backing up (the zip each directory is nice when you have TONS and TONS of files). You can then copy to a network share or ftp server. Then you can set a schedule for it to run at 3am or whatever.
Again, I use this at work to sync our file shares and cross-backup files from server to server. I then, being paranoid (or smart), burn DVDs of the stuff every so often and get them off site.