Have you seen http://schemes.zwapp.com/.json?page=1 There is the beginning of some hope: http://gigaom.com/2011/06/09/zwapp-builds-a-social-network-f... its a database of all the apps that use custom url schemes.

You can also use javascript bookmarklets to compose with any webapp (webpage).

Hopefully one day apple will expose a framework that will allow users to do in app user level scripting for all apps. And maybe even allow cross app scripting with very well declared uses by responsible / licensed people.