I have a Phonegap (cordova) application where I want to load some external webpages within the phonegap WebView and I have other external webpages that I want to load in saf
Just catch all links in your javascript that have target="_blank", and pass them to window.open with the '_system' param. This will work on both iOS and Android.
$(document).on('click', 'a[target="_blank"]', function(ev) {
var url;
ev.preventDefault();
url = $(this).attr('href');
window.open(url, '_system');
});