Popups are executing malicious code using a flaw in IE to place a trojan horse on your computer. This trojan horse looks for websites where you might transmit important data, like bank websites, then captures your information as you enter it. This is very serious because there is not a patch issued from Microsoft for this problem.
Get the full story at ZDNet.
If you continue to use IE, at least put your security settings at High. Otherwise, I would suggest using an alternate browser, like Firefox or Mozilla.