Hi Justin -
As another idea rather than file-based-storage, if your specifically wanting to move away from SQL, would be to store the preferences in an IMAP folder.
A project "IMHO Webmail" (a Roxen webserver module) did this a few years back (and there's bound to be others).
The benefit of this is that the preferences are distributable, yet still "simple files" -- so you could have multiple webmail servers accessing them; and not need to worry about preferences getting out-of-sync between them.
/Mark