Pop-up windows are one of the biggest UI blunders ever. They create seperation from your website, they detract from the main content, and they are far from a 'seamless' data entry mechanism.
First, never, ever, ever have the browser pop up a new window in the first place. Ever. There is absolutely no reason for it, and there are easy ways around it that can avoid pop-up blockers totally screwing your user experience: for example, modal windows. They're an extremely easy mechanism to put in place (you can even use frameworks, like Scriptaculous or components from the Ajax toolkit for .NET), and they get around pop-up blockers. And, not only that- but you don't have the issue of not being able to send commands to your parent window! In this, it lends itself heavily to Ajax applications, in that you can also update content on the main page after submitting data from the modal. Seamless transitions are the best; make your web app behave like a desktop app. You also know that your user won't be messing with anything on the parent, out of order with the pop-up. It fits everything in place and creates a nice flow to the website.
So, please, please remove your pop-up windows and stop keeping your users from having to disable pop-up blockers!