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When you copy a link OmniWeb sends a lot of data to your paste board. This includes the title of the link and of course the URL itself. It's then up to the receiving application to parse that information into something usable. Most rich text applications are going to take the title and make that link to the URL--just like a link on a webpage.

If the page you're linking doesn't have a title it uses the url which is truncated if it is too long. Personally I think this should be the linked text you copied out, something for the future i guess.