I am trying to allow a URI to be registered to open up with my app. Like the PatternRepository on the Blackberry and the CFBundleURLName/CFBu
You could always try sending your emails using HTML and then use an tag around to create the URL. I don't think there is a way to change the way the Gmail or Mail parse their text, since they probably use the Linkify class.
Another option would be use use http:// and then just parse for a specific custom subdomain which would provide your users with the option to open in a browser or your application.