I’m running Win2k Advanced Server sp1 and IE5.5 sp1. I just went to hotmail and got a pop up when I first logged in (for ebay), but not as I navigated folders. You could turn off javascript by going to Tools|Internet Options|Security|Custom Level|Active Scripting but you’ll probably lose functionality on a lot of sites.
I’m sure the guys at MS have done it as a way to make advert money. Another thread also talked about pop ups like this. It seems to be a growing trend.
Still better than actually paying for the net though.