Except dropbox will be totally unaware and try to access it.

What i envisionned was more like a "control center" app of all the outgoing (and incoming) pipes from your FS to syncing systems, with both last syncing time, configuration, etc. A little bit like what's already happening for mail and calendar integration into iOS applications, only for files and on the desktop.

This isn't really a great solution when I have files that are autogenerated. I either have to have the default group be "cloud" and then go back and chgrp these files when they are generated so they don't sync. Or I have to have the default group be something else, and inevitably forget to chgrp for files that I do want backed up.

Some file-system level property could work, but the semantics of the archive bit don't match. For files I want to be ignored, I don't think it makes sense to mark them as backed up, which is what the archive bit was designed for.