As John Gruber pointed out last week, you can move your Yojimbo database into your Dropbox folder for real-time backup if you use a Symlink. For those who aren’t Symlink savvy, here is an Automator workflow that will take whatever folder you pick, create a symlink for it, and save it in a new location of your choosing.
This is commonly done to keep apps like Yojimbo or Things in sync across multiple computers. But I only use one computer so I don’t need to sync. However, I very much like the fact that now my Yojimbo database and MarsEdit drafts are backed up at all times, not just nightly.