I’m still using my rsync process and I’m very happy with it. I haven’t tried any of the other suggested tools…I meant to but I guess my motivation wasn’t high enough because I’m happy with my process.
Whatever way you choose, I think it’s useful to not deploy all files and folders you have in dev mode. I think it’s good to have some sort of build process with grunt, gulp, custom scripting or whatever you like.
As far as content backup is concerned – @texnixe, rsync can do this, either manually or automatically with some sort of cron task. You could also zip or tar your target files and folders and scp them somewhere. Lots of options – tyranny of choice 
Edit: forgot to mention that you obviously need ssh for rsync to work. While more and more providers offer ssh access, clients may only have simple webspace with ftp access.