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Sync with iCal was originally invented as a way to get basic "to do" list info to and from the various PDAs that sync with iCal, before the iPhone SDK was available to us. (And of course, it's still useful for people who have a PDA but no iPhone.) As a side effect, that same data will show up in the MobileMe calendar.

Sync with Server is for syncing between OmniFocus and OmniFocus. (laptops, desktops, iPhones, iPod Touches) MobileMe's iDisk is just a convenient place to share that data. You can also use BingoDisk or various other WebDAV services. This data is in the OmniFocus format, so MobileMe doesn't get any iCal information out of it. On the other hand it carries ALL the OmniFocus info, rather than being limited by just the data iCal understands.