This has been really fickle with Cordova/PhoneGap in the last few releases, I believe because of the InAppBrowser work which might be a solution for you.

What is working for us to launch in the external browser is:

window.open(http://myurl.com, '_system');

In our case, we want to find all external links and launch them in Safari/Chrome (and keep internal links in our Angular router). This probably isn't the most elegant solution, but we are doing this right now by capturing input events on the links and taking over the behavior like so:

        $(document).on('mousedown','a', function(e) {

            e.preventDefault();

            var elem = $(this);

            var url = elem.attr('href');

            if (url.indexOf('http://') !== -1) {

                window.open(url, '_system');

            }

        });

I hope that helps you a bit.