I have chosen "Block popup windows" in Safari's security tab, yet there are a couple of sites for work that still use popups for login etc. Is there a way to add exceptions (in advanced settings or directly in the plist file perhaps?) Or maybe via a Safari extension?
There isn't any exception list for popups in Safari. It's an "all-or-nothing" approach for now.
I recommend telling Apple your thoughts on the Safari feedback page: http://www.apple.com/feedback/safari.html
EDIT 12/20: This answer is correct as of the time it was written. Since then, Apple has added the ability to control popups per site. This answer by @matt-chandler is the correct one for newer versions of Safari. I'm leaving this answer here in case it helps people on older versions of Safari.