Most popups are called by JScript links, so a first step to reducing their appearance is to simply turn off the Java Add-On except when you need it. (In Internet Explorer it's at Tools|Manage Add-ons) Most AV makers (and even Microsoft) recommend turning Java off for routine browsing anyway, simply because it's too powerful/versatile to be left idle for use by malware.

Internet Explorer has a built in PopUp Blocker that is reasonably effective, although it doesn't stop them all. (Tools|Popup Blocker or Tools|Internet Optiotns|Privacy Tab).

You should be aware that for many sites, the site receives a small payment each time you click on an ad but also often receives a small (often smaller) payment simply for each time the ad is displayed. Since only a small percentage of people "click," but everyone "sees" the ad (in the absence of an aggressive Ad-Blocker) the preferable procedure from the standpoint of the site is for you to allow reasonable numbers of the ads to appear, and just ignore them. (Sort of like when your spouse speaks but you just don't hear it? Any married person can explain how, a week after the honeymoon.)

It's difficult to know what "payment model" a site is using, but for most sites a "fairly friendly" explanation of the effect of ad blocking is at:

Why Ad Blocking is devastating to the sites you love (Too loong to post, but not hard to read.)

While popups are annoying, the tracking cookies are probably the most "invasive" for most people. A GOOD AV program should minimize their effect better than most add-ons you are likely to find.

John