The way you can do this for "http://" URLs (and what I think Apple and Spotify do) this is to:
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Register a custom URL scheme like the other answers have shown.
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Set up your HTTP URL to point to a real webpage.
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Put a script on that page to redirect to your custom URL if is on iOS.
For example, here is a sample page which will take you to the Twitter app for a particular user or the Twitter website depending upon if you are on the web or on your iOS device.
Try it out here: http://bl.ocks.org/d/3153819/?mckamey