You’re referring to two different things. When you visit a site and a new window pops up, JavaScript is being used. When you click on a link in this forum and a new window pops up, that’s HTML. You can go ahead and disable popups in your browser and you’ll still be able to click on links in posts just fine.
My favorite popups are the ones that have somehow replaced the blue window toolbar with a picture of the blue window toolbar. So if you try to close the thing using the button, you’ve just clicked on their ad.