SparkleShareYou can create a GIT repository on your own linux server using included dazzle tool. This tool installs GIT if needed, creates a new user storage for this purpose and adds authorized keys created on client machines. It can also add more trusted key fignerprints - more clients. And finally it creates shares (projects). After a share is created, you can "mount" it on your client machines. SparkleShare watches for changes and after they are saved completely, they are automatically transferred to the server.
Now for the fun part.. download and install Link Shell Extension and use hardlinks to mirror requested config files to app data locations. On other machines, remove the current config files and create hardlinks to the mounted locations. The only downside is you can't synchronize Windows registry changes, so if you plan to synchronize eg. PuTTY, you need to use a portable version, that exports registry to REG file when the app is closed. IMO small apps like PuTTY portable can be mirrored whole, not just the reg file; also the updates are pretty easy - you just update once and other machines are updated as well.