One trick I do with syncing is have sandboxie only share the bookmarks between the sandbox and the actual Chrome or Firefox directory. Then, the sync program never sees the cookies and cache or other stuff thrown on there. Plus, it provides better privacy, because it assures that everything (cookies, cache, etc) is gone... because it was never there in the first place. Of course, this does nothing to stop web browser fingerprinting (a la EFF's Panopticlick), but that is a digression.
I do agree with you -- automatic sync applications have a place, especially if they can store previous versions somehow. That provides an effective third layer of protection (the other two being a backup nightly to disk and backups of documents offsite to Mozy, Carbonite, or another place.)
I use SyncToy on one machine, but it cannot do continuous syncs... only on a schedule you manually create, so if you do a lot of changes on a document, then accidentally delete it, it might be of little to no use.