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If the alternate solution is working well, then at the moment there's not much difference. There have certainly been people who have encountered WebDAV installations that didn't get along with OmniFocus. At some point in the future there may be additional services offered by Omni (perhaps being able to mail actions to an address to get them into your database without having to have a Mac running Mail 24/7, for example); probably you would need to use their server to take advantage of that. Given they've committed to providing the basic sync service for free, not much disadvantage to using them, either.