I found that the selected answer works for the browser apps but I was having issues with the code working in non browser apps that implement a UIWebView.
The problem for me was a user on the Twitter app would click a link that would take them to my site through a UIWebView in the Twitter app. Then when they clicked a button from my site Twitter tries to be fancy and only complete the window.location if the site is reachable. So what happens is a UIAlertView pops up saying are you sure you want to continue and then immediately redirects to the App Store without a second popup.
My solution involves iframes. This avoids the UIAlertView being presented allowing for a simple and elegant user experience.
jQuery
var redirect = function (location) {
    $('body').append($('<iframe></iframe>').attr('src', location).css({
        width: 1,
        height: 1,
        position: 'absolute',
        top: 0,
        left: 0
    }));
};
setTimeout(function () {
    redirect('http://itunes.apple.com/app/id');
}, 25);
redirect('custom-uri://');
Javascript
var redirect = function (location) {
    var iframe = document.createElement('iframe');
    iframe.setAttribute('src', location);
    iframe.setAttribute('width', '1px');
    iframe.setAttribute('height', '1px');
    iframe.setAttribute('position', 'absolute');
    iframe.setAttribute('top', '0');
    iframe.setAttribute('left', '0');
    document.documentElement.appendChild(iframe);
    iframe.parentNode.removeChild(iframe);
    iframe = null;
};
setTimeout(function () {
    redirect('http://itunes.apple.com/app/id');
}, 25);
redirect('custom-uri://');
EDIT:
Add position absolute to the iframe so when inserted there isn't a random bit of whitespace at the bottom of the page.
Also it's important to note that I have not found a need for this approach with Android. Using window.location.href should work fine.