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If you're syncing OmniFocus frequently on your various machines, but the Settings screen in your iPhone app is still telling you you have lots of zip files, you'll want to do the following.

On one of your Macs, open the Sync pane of OmniFocus' Preferences. Press the "Show Clients" button. You'll see a sheet slide out, listing the devices that your sync server knows about, as well as the most recent sync date for each of the devices.

Each device you're syncing should have exactly 1 entry in the list; if you see any duplicates, you'll want to delete the entry with the earlier "Last Synced" date. Additionally, you'll want to remove any entries for any Macs, iPhones, or iPod Touches that you're no longer syncing. (A device you've given away or sold, for example, may still have an entry in the list.)

Once you've removed any duplicates or stale entries, close the sheet and sync your Mac. Wait an hour, and sync the Mac again. If you sync your iPhone at this point, the database should have fewer zip files. (The one-hour wait is required to force OmniFocus to compact your database during the second sync.)

Last edited by derekr; 2012-02-13 at 08:16 AM.. Reason: OmniFocus for iPhone no longer has a setting for manual-only syncing.