It depends on what you call "popup window". Usually, this term means the concept of creation of a new browser window (which can also be a browser tab) using
In most cases, it would be a pretty bad idea. It's intrusive (you decide where to place new content, but, in the spirit of the Web design and tradition, the user should decide that), inconvenient (the user would need to remember where new content is and switch between window; don't forget that some may have dozen of other pages open), and finally, many will block popups (this is a usual feature of browsers, often enabled via browser plug-ins).
Much better alternative is so called "modal pop-up", which simulates modal behavior on the same page. In addition to jQuery
(Dialog | jQuery UI
]), there are many, with different effects, such as transitions, and, notably, dimming: modal popup
Please see my article: Modal Popup From Scratch
In this article, not only I explain how it works, why it works, but provide the motivation.