I use scp to backup the folders I'm interested in. I use git to manage sharing data between machines. (Again, just the stuff I'm interested in.)

I don't keep 100% synchronisation between machines. I don't back everything up. I'm happy working at this level of granularity because it allows me to stay selective and not accumulate cruft due to relying on an automated backup of my entire drive. (In my case, backing everything up would result in a lot of useless noise.)

I'm not saying it's for everyone, but it works for me.

You might want to look into rsync as a replacement for scp.

Version 2 is built in, but if you follow the directions at:

http://www.bombich.com/rsync.html

you can build a newer rsync that syncs all metadata.