Instead of using a link target which breaks XHTML 1.1 validity, you can create a popup link using jQuery.

To do this, you can use XPATH in jQuery functions

Now, in your template file (e.g. node.tpl.php) insert this code:

drupal_add_js('
$(document).ready(function(){
  $("a[@href^=http:]").click(function() { 
    window.open(this.href); 
    return false; 
  }); 
});', 'inline' );

Now all external links on your site will pop up in a new window, but internal links will not be affected, provided they are not programmed with "http:" in front of them (most Drupal automatic links are not).