If you switch popups to only show in new tabs (requires a bit of about:config editing, or using the Tab Mix Plus extension) this eliminates some of the more obtrusive flashing.

Has the added bonus of keeping windows tidy -- although it's a matter of taste, I prefer even having wanted pop-ups going to new tabs rather than whole new windows.

NoScript can be very, very handy for these things, although I find it necessary to run it in blacklist-only mode (whitelist would be more secure, but is too intrusive.)