JavaScript allows you to create (open) new windows. In these windows you can place whatever HTML code you wish http://blazonry.com/javascript/windows.php
When writing content for your site you might want to give some tips or explainations for particular words or phrases. http://www.smartwebby.com/DHTML/tip_boxes.asp
Ever want to place a link or button on your page that will close the window to make it easier on the user? http://www.ethicsdesigns.com/tutorial_close_window.php
This is a robust DHTML Window widget that replicates the look and functionality of a traditional pop-up window http://www.dynamicdrive.com/dynamicindex8/dhtmlwindow/
In this tutorial I will show you how to create a layer based popup window with JavaScript. http://www.javascriptf1.com/tutorial/javascript-popup-window.html