For the same problem I've used existing webintent plugin, modified the android manifest file - add those lines to activity

<intent-filter>

    <action android:name=android.intent.action.VIEW />

    <category android:name=android.intent.category.DEFAULT />

    <category android:name=android.intent.category.BROWSABLE />

    <data android:host=example.com android:scheme=http />

</intent-filter>

and modified the index.html ondeviceready:

function deviceReady() {

    window.plugins.webintent.getUri(function(url) {

        console.log(INTENT URL:  + url);

        //...

    }); 

}

EDIT

I've just noticed a behavior which may be unwanted. When you open the app using the link (intent) from another application, it will (in many cases) create a new instance and not use the already running one (tested with gmail and skype). To prevent this a solution is to change Android Launch mode in config.xml file:

<preference name=AndroidLaunchMode value=singleTask />

(It works with cordova 3.5, not sure about the older version)

Then you need to add one more function to ondeviceready:

window.plugins.webintent.onNewIntent(function(url) {

    console.log(INTENT onNewIntent:  + url);

});

This one is triggered when the app was already running and was brought to front with intent.