Heya Kieran,
That question is a tough one to answer. In general, the use of pop-ups should be discouraged. More and more sites use them for ads and so people just see a popup and close it most times. At least that is what "usability stu***s" say.
What I recommend, is using pop-ups as a last means. See if there are other options, then use a pop-up as a last resort. One good use for pop-ups is when you are loading a flash animation or game.
Basically, use pop-ups where it makes sense. I can 99% guarantee you will never see an ad pop-up on HTMLCenter. At least until someone pays us enough so we can all retire on a small island with some models and a T1 line.
Good luck,
Allen