Versioning is a key consideration, but I’ve honestly never considered the implications of versioning snippets. That’s a great point (and probably a great idea). IMO, if we do versioning, we’re going to need to store versioned elements in the DB for ease of working and simplicity.
Then again, based on seeing Victor’s bootstrap installer (imagine only uploading a 3Kb file to perform an install...it’s really sweet with MD5 checks and .zip decompression of remotely retrieved latest file versions, etc.), I think we could accomplish something very similar with proper filesystem designs.
Furthermore, we could create a backup module that could trigger not only a DB dump but also a .zip archive and remote FTP transfer ... or email to your a gmail account for free remote backups.
As far as plugins and modules go, however, I would love to see them on the file system for no other reason than installing them could become a simple matter of dropping in a folder (like a Photoshop plug-in) and then telling the Manager to activate them. Whether that involves inserting the code into the DB is another thing entirely, but worth thinking about nonetheless.