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Personally, I like that OmniFocus (and Mail, iCal, and Address Book, ...) stores its data in ~/Library and not Documents. I want Documents to just contain the documents that I explicitly create. To me, OF is not "document-based" application. I can't do anything with my OF data apart from manipulating it with the application, and I can't have multiple sets of data open in the application simultaneously.

Oh, and I clone my entire hard drive every night. SuperDuper is.
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Cheers,

Curt