I would strongly suggest to never, ever open a link in a new window. The user doesn't expect it and many users don't like to clutter their taskbar with another window. Some have solved that problem by making an addition like "(new window)" to the link. Keep in mind that without a browser plug-in there is no way to stop it from opening in a new window. Normal links however, can be opened in a new window or tab if that is what the user wants. You want to make the user as comfortable as possible while browsing your site. If your visitor wants a link opened in a new window, they can handle it themselves.
This spawns a question: what about links to outside sites? Some might argue that those should open in a new window so the user doesn't leave your site. After all, you want them to continue browsing your site right? Certainly, but it's still unexpected. A better idea may be to put all your links to other sites together in either a links page, in a section of a menu clearly titled "Links" or something obvious, or appending an image to each outside link like Wikipedia does (see the "External links" section at the bottom of almost any article). Making the link itself the name of the outside site is another solution. Whatever you do, make it obvious. If your visitors are not ready to leave your page, they either won't click, or will open it in a new window or tab themselves.
Photo galleries
Another place new windows are often used is for photo galleries. Clicking on a thumbnail picture spawns a new window with a bigger version of the same picture. While this is more accepatable, there are other ways. Consider one big image, with linked thumbnails along the bottom or top that will replace the big image. The images below show examples of this method.

Examples of photo galleries
Or consider using a combination of JavaScript and CSS to give the impression of a popup, without actually having a popup. I implemented this myself on my personal site's picture page.
Acceptable uses
There are some acceptable uses of popup windows, such as posting comments on a blog or message board. Using JavaScript, you can open a new window of a certain size without a menu or toolbar. If this is absolutely necessary, make sure the size of the window is as small as possible.
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