Similar to [backing up your 1Password library with Dropbox][1pass], comes in [this tip for Yojimbo][link]. Essentially the trick is to move your Yojimbo data to the Dropbox folder, then put up a symlink in the old folder location, like so:
mv ~/Library/Application\ Support/Yojimbo ~/Dropbox >ln -s ~/Dropbox/Yojimbo ~/Library/Application\ Support/
I don’t see why the technique employed here couldn’t work for any number of applications that use a centralized data store.
[link]: http://groups.google.com/group/yojimbo-talk/msg/dfffd469a71b4b9e?pli=1 “Sync problem solved! – Yojimbo Talk | Google Groups”
[1pass]: http://extrafuture.com/2010/03/17/protip-automatically-backup-your-1password-keychain-offsite-with-dropbox/ “How To: Automatically Backup Your 1Password Keychain Offsite With Dropbox”