Ideally I'd like this control app by app and I'd still like the ability to override it on a case by case basis. For example, I search a business name in safari and click on a link that happens to be to yelp, I don't want the yelp app to auto-launch every time that happens but there may be an occasion when I do (e.g. I want to order food or make a reservation). Give me something like the "there's an app for that" panel that shows up at the top of some websites (not a pop up dialog please) giving me the option to hand off to the app. Maybe even make that prompt configurable so for some apps I never have to see it (e.g. LinkedIn I would never want to redirect). On the other hand, Open Table would be an app I always want to launch (I'd never go to their web site other than to book a table so may well put me right into the app) so configuring it to redirect automatically would be my preference.
In other words I think this idea and then some.