Why not just move the Preferences folder to your Dropbox then make a symlink?
I don’t move the folder, I just put a symlink in the Dropbox folder. That seems to work great, am I doing it wrong?
– edit: Ah, I just had a epiphany. I only have one computer, I use Dropbox for backup and to occasionally access one file or another when I happen to have to use friend’s computer, not to sync several computers. It makes total sense to put the “original” files into Dropbox and to put symlinks on the individual computers if what you want to do is syncing, not backup. Is that right?
Also some apps let you specify where their preferences folder is located by holding down the option key when you launch them. Then you can set them to use a folder in your dropbox.