Unfortunately, custom URL handlers on iOS do not work.
You can define custom URL patterns that your application will open, but you cannot make your application the designated handler for specific domain names so that opening this domain in Safari will automatically launch your application.
To be clear, the scheme is a bit before the domain name, for example http:, so you can make your application a handler for the URLs starting myapp: for example. Obviously, no real URLs start with myapp:, except for those that you specifically designed for your application - that’s the whole point.
Unfortunately, these URLs will only work with your application, they cannot be opened in Safari if your application is not installed. iTunes, Google Maps, Youtube, etc. it all works on the iPhone, because Apple hard coded them as special cases, but they do not make this mechanism available for third-party applications.
To register a custom schema for your application, follow this guide: http://iosdevelopertips.com/cocoa/launching-your-own-application-via-a-custom-url-scheme.html
Instead, you can create a regular web page that uses javascript to discover the device’s user agent, and if it redirects iPhone to the user’s application’s schema automatically using document.location = 'myapp: ...'. I'm not sure what will happen if you try to redirect to a custom URL scheme if the application is not installed. It may not do anything that would be ideal for you, or it may cause an error or go to a blank page, in which case you better not see a message like "click here to launch the application, or click here to download it from app store, "which seems to make most sites.