The best way to open links in a new URL is actually with window.open. Just set the target as “_system”:
window.open("http://stackoverflow.com", "_system");
Before I found this in the docs, I actually wrote a plugin to do the same. I’m going to leave this answer here, because this would give you much more granular control over handling of links.
With PhoneGap 2.3+, I was unable to get URLs to open in Mobile Safari in any way. Using _blank didn’t work, and I tried window.open(url, ‘_blank’), but this now opens the URL using the InAppBrowser plugin (which pretty much sucks). I thought it was interesting that that one used a plugin though, so I decided to write a plugin to open URLs using the standard method of opening URLs in iOS apps. You can see/grab the code on this gist here: https://gist.github.com/typeoneerror/5097118.
In my example, I wired up links that have a class called “_blank” with jQuery and opened those URLs with the plugin call:
// execute the plugin called OpenUrl, signature:
// exec(successCallback, errorCallback, pluginName, pluginMethod, params)
cordova.exec(success, error, "OpenUrl", "openUrl", [url]);