Seems like Dropbox has already solved this problem on mobile devices. Using the Dropbox client on my Nexus phone or on the iPad, I can read or edit a file, and then mark it for offline use which keeps it in local storage, or just leave it alone, where I assume it's eventually deleted from the cache.

It's pretty transparent and intuitive. I would think this could be done on desktop / laptop systems, maybe via an optional client, with all files set initially to a no-sync value.