There is hardly ever a reason to use them, when there are so many good lightbox solutions and the like out there.
Woe be the day when some HTML5 crap starts building those in so I can't block them, like they're doing now with autofocus and auto-fill in forms. Hate, hate, hate.
How does a blind person with a screen reader access the info in a popup, for example?
If it's built by the browser (like you get with actual new windows, alert() popups, etc), focus moves to it and it's announced. New users are probably confused but, new users are confused by everything anyway.
Some people have been playing around with the new ARIA live regions but I haven't seen this actually work anywhere yet... application roles stole navigation and reading abilities, alertdialog was buggy everywhere, someone somewhere always broke...
...however I expect these will get ironed out and fixed eventually, and screen reader users will be the easier group to write for... everyone else will be the problem.
I guess it was "let's try to make things as DIFFICULT and BIZARRE as possible for users" day. Let's make sure it works so UNLIKE any NORMAL form that people screw it up a few times before they actually get it right.
Oh, I know designers love trying goofy new things, but this is why they should all get chained down to a chair and forced to learn basic. freaking. usability. before being allowed to touch a keyboard. Oh wait, I mean mouse, these people only know how to use mice. ARG.
And on that note, I agree 100% with JJ that it's kinda getting retarded whenever someone asks "how do I do popup type X?" that more than one response has to be mentioning how horrible the things are. One is probably enough, and if the OP already says "yeah I know people hate them" then I don't see where the benefit is of ranting further about them in that thread. (though, the latest thread, where the OP kept insisting that his popups were special and adorable and not annoying at all in any way, that just made me laugh really hard. Yeah right, bro)
When someone says "I want to cut my own head off" and one person say "that will be painful and cause your death" and the OP says "Yeah but I really wanna, it's a science experiment" then we've done our job and now anyone who wants to explain to the poor sod how to cut his damn head off, do so. We're not required to spend 16 out of the 20 responses on how much it really sucks to have your head cut off, are we?
If users hate popups, they'll do what the rest of us do: leave. They are usually on commercial and personal sites, not sites we're forced to use like our utilities, banks, and government sites (if they are, then we do get to spend 19 out of the 20 responses complaining about how much popups suck balls and bring Satan back to Earth and cause wee orphan children to contract cancerous forms of herpes, of course), so we generally have the option to leave.
Authors are allowed to destroy their own sites, especially if they live in countries without any demands that they actually build accessibly and well.
BTW: next site I get a retarded popup in, I'm actually going to spend time writing them an angry letter just so the site owners can enjoy my colourful language. After all, they asked for it, knowingly.
*edit oh, I need to add a word to my post to make it complete: