How to open pop up window in javascript in drupal 6?
Use the Colorbox module.


  Colorbox is a light-weight customizable lightbox plugin for jQuery. This module allows for integration of Colorbox into Drupal.
  
  Images, iframed or inline content etc. can be displayed in a overlay
  above the current page.


You need to activate the iframe method and add the custom iframe class to your link.