[Ken Case]

I'm not sure what could have caused this data loss; the only time OmniFocus removes its database is if you click on the Reset Database button at the bottom of the Settings screen, and that button prompts to confirm that you're certain you really want to do that.

But since you lost data from other applications at the same time, it sounds like there's some other system-wide issue to blame, and unfortunately there's nowhere OmniFocus can store data on the device itself which would be safe from that sort of problem.

The only way to prevent this sort of data loss, then, is to make sure it gets backed up to another system. The OmniFocus database does get backed up with everything else in iTunes, and you can restore it along with the rest of your system there, but that takes a long time and overwrites the rest of your system in the process.

Instead, my strong advice would be to set up synchronization with MobileMe or some other WebDAV web server, even if you're not synchronizing with the Mac version of OmniFocus. That way, even if you lose everything on the phone itself you'll be able to recover it again quickly, simply by re-synchronizing with the server.

Sorry for your data loss, and I hope this helps!