As a user, I must admit it, I found them annoying. Not as bad as pop-under, but disturbing most of the times. I'm reading and getting quite a lot of opinions on pop-ups in these days since I'm writing a column for an Italian portal on the topic. Someone predicts that pop-ups will disappear in one year time (exactly like e-mail marketing, see this post) and I agree with this opinion if I refer it to big portals, while I believe pop-ups will still be used by many small and medium size Web sites.
Anyway thanks to a link on Marketing Profs I've also found an academic paper on pop-ups that investigates timing of pop-up promotions that customers encounter while browsing informational websites. They might not be as bad as they appear to be. Timing as well as context are important issues when talking about advertising and online advertising in particular, and might offer interesting points in order to reconsider the future of pop-ups.
The study is by Wendy Moe of the University of Texas and can be downloaded for free here (.pdf). Eventually a free academic paper! Thank you Wendy for sharing!