[whpalmer4]

The following proof of concept seems to do the trick for me:

tell application "Mail"
	tell message viewer 1
		tell message 1 of inbox
			set theStr to "message://%3c" & message id & "%3e"
		end tell
	end tell
end tell

tell application "OmniFocus"
	tell front document
		make new inbox task with properties {name:"test", note:theStr}
	end tell
end tell

It produces the same URL text that the OmniFocus Clip-o-Tron does. It won't work on an iOS device, but it should work for the Mail app on the Mac. If you're trying to do links to multiple messages, you need to extract the message id from each one in turn and generate a link.