[Brian]

There's an issue in the OmniFocus for iPhone 1.0.2 and earlier which causes the sync process to take longer than it should. We'll have a fix in the 1.0.3 release, but for the time being, you'll want to do the following to work around the problem.

Sync all your desktop computers, then run the attached applescript attached to this post on whichever Mac has the most up-to-date info.
(You can run an applescript by opening the "Script Editor" application, opening the script file, and pressing the "Run" button.)
Next, open up your iDisk (or whichever location you're storing your sync database at) and rename that copy of the OmniFocus database to "OmniFocus-Old".
(This allows you to revert to the data at some point in the future if necessary.)
Sync from the same machine you ran the applescript on.
Launch OmniFocus on your phone and start a sync; when asked whether to use the 'local' or 'server' copy, choose 'server'.

Your syncs should now take a reasonable amount of time again.

[Brian]

I'm posting the text of the applescript here, for folks who don't want to have to create a forum account in order to download the applescript file.

They can copy the code below, paste it into a new Script Editor document, and save and/or run the script that way.

set temporaryArchive to POSIX file "/tmp/CoalescedDatabase.ofocus"
tell application "Finder"
	try
		-- Make sure our temporary archive doesn't already exist
		delete temporaryArchive
	end try
end tell

tell application "OmniFocus"
	-- Find the database path
	set databasePath to file of front document
	
	-- Save this database into our temporary archive
	archive front document in temporaryArchive without summaries
	
	-- Close our broken database, open the repaired temporary archive
	close front document
	open temporaryArchive without using cache
	
	-- Replace our local database with the coalesced copy
	tell application "Finder"
		delete databasePath
	end tell
	archive front document in databasePath without summaries
	
	-- Open the coalesced database
	close front document
	open databasePath without using cache
end tell