Yep, if you don't want to use Sync, user.js is an alternative. It's also helpful for sharing settings across multiple profiles. (For the latter, I do wish there was support for including other files...)
There is a user.js project on github[1] maintained by ghacks.net community members that provides a source of documentation for many settings. It's also useful as a way to monitor new and deprecated settings.
[1]: https://github.com/ghacksuserjs/ghacks-user.js
