The new window thing becomes moot as more and more browsers open those links as new tabs by default anyways.
I learned through user testing to open PDFs in new windows though. All the users we tested were generic Windows users who used IE. If we didn't abuse target or use JS to open the PDF in a new window, the users always closed the whole browser while assuming they were only closing the PDF. Every time. Luckily our test browsers remembered the last-opened windows...
I find the idea of using outdated Frameset attributes to open new windows quite funny, because we're not using _top or any of the other frame names (though I've seen _self on websites still! Amazing).
It's just retardation and finding out 2 hours later that you've still got a window open of a site you left 2 hours ago means, as Crusty would say, 2 things, and Jack left town.
As a general rule I only open off site links in new windows if I do it. Or just recently I added a FAQs page. I have 50 click to open facts and each has an included link to more info. I used target blank there too even though they are inter site links.
Thank the gawds my browser can override whatever some webbie writes. I can't think of one good reason why I would want a separate window for ANYTHING. Well, unless I was using IE6 which doesn't have tabs. New windows had more reason to exist with IE6 around.
I don't hate that idea as much as I used to, but if there were more than say, 3 links on the page I was doing that to, I'd still go back to an external JS file who would find all the links for me and grab their href values and whatnot. Cuz I'm lazy.