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