I use a pop-up window on some of my applications that have a directory search that assists the user in filling in forms (like a person's correct name, e-mail address and their manager's name and e-mail). It just doesn't make sense to do these kinds of functions by going off to another page altogether.
Also, I use a pop-up calendar to input dates, especially when I need an alternative to a DHTML version that doesn't work with Netscape which is notoriously bad when displaying over (or more correctly, under) form elements.
Also, many sites have "customer examples" links, like web developers. You don't want your visitors to have to leave your site everytime they click on one of your example sites. They'll quickly get tired of going back and forth with their browser back button.
I also have news items that open in new browser windows when they are offsite. I definitely don't want my users leaving my site as soon as they arrive because they want to follow up on a news item on the home page.
There are a million instances where opening a new browser window (which is what a pop up is) makes more sense for the user than going off onto another page and losing the page their on.