I think I've got a working solution.

 <!-- links will work as expected where javascript is disabled-->

 <a class="intent"   

    href="http://facebook.com/someProfile"   

    data-scheme="fb://profile/10000">facebook</a>

And my javascript works like this.

note: there's a little jQuery mixed in there, but you don't need to use it if you don't want to.

(function () {



    // tries to execute the uri:scheme

    function goToUri(uri, href) {

        var start, end, elapsed;



        // start a timer

        start = new Date().getTime();



        // attempt to redirect to the uri:scheme

        // the lovely thing about javascript is that it's single threadded.

        // if this WORKS, it'll stutter for a split second, causing the timer to be off

        document.location = uri;

        

        // end timer

        end = new Date().getTime();



        elapsed = (end - start);



        // if there's no elapsed time, then the scheme didn't fire, and we head to the url.

        if (elapsed < 1) {

            document.location = href;

        }

    }



    $('a.intent').on('click', function (event) {

        goToUri($(this).data('scheme'), $(this).attr('href'));

        event.preventDefault();

    });

})();

I also threw this up as a gist that you can fork and mess with. You can also include the gist in a jsfiddle if you so choose.

Edit

@kmallea forked the gist and radically simplified it. https://gist.github.com/kmallea/6784568

// tries to execute the uri:scheme

function uriSchemeWithHyperlinkFallback(uri, href) {

    if(!window.open(uri)){

        window.location = href;

    }

}

// `intent` is the class we're using to wire this up. Use whatever you like.

$('a.intent').on('click', function (event) {

    uriSchemeWithHyperlinkFallback($(this).data('scheme'), $(this).attr('href'));

    // we don't want the default browser behavior kicking in and screwing everything up.

    event.preventDefault();

});