Unfortunately the pop-up blockers in most browsers no longer work. They blocked an older style of pop-up that almost no one uses anymore.
Advertisers have created new versions based on javascript. Turning off Javascript will block them, but it also blocks many of the other useful features that have become standard.
There are ad blocking apps for the iPad. They work by detecting where the ads come from and redirecting content from those sites to the void. If I remember right the two most mentioned ones are AdBlock and Webloc.
It's an all or nothing solution that uses the network proxy settings on the iPad. Ad content for the included sites will be blocked for all the iPad's apps, not just Safari.
My solution is to stop going to sites that have annoying block-the-content style ads. Or at least minimize visiting them if they can't be avoided. I can understand a site's or app's need to generate income with ads, but I see no reason to reward them for making me jump through hoops to read content. I have better things to do with my time than wait for a mandatory ad to time out and let me read.
A note to advertisers who think these ads are effective. It's true, I do tend to remember them better. It's also true that the product goes to the bottom of my list of possible purchases. It would have to be something I can't do without, and have no decent competitors before I'd buy it.
Of course, I might not be a typical consumer.
Sorry for the rant.
