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Thanks Yury - it's odd, but you used to be able to do exactly this in OmniFocus by simply dragging the email into a note, there is a thread discussing it where it is said:

Originally Posted by Alex Brown View Post
In leopard you can drag a mail item into the note of an action, which creates a link back to the mail item. Almost there!.
However that was back in 2007, and there have been a few subsequent comments asking how to do it, so I assume that functionality is lost.

Assuming the dragging option is no longer an option, I'll happily go with your script, I couldn't get it to work until I removed the inner "tell application "Mail" to activate" loop, hence:

HTML Code:
tell application "Mail"
	set theSelection to selection
	set theMessageID to the message id of item 1 of theSelection
	set theMessageURL to "message:%3C" & theMessageID & "%3E"
	set the clipboard to theMessageURL
end tell
To me that's probably good enough, I can cope with the pasting, as it means I now have an application that extracts email links so I can use them in either OmniFocus or OmniOutliner