So, here's a related question that presents a possible use case.
Let's say John Public is moving from an application at one subsite to an application at another subsite, and the business logic requires that he re-authenticate to ensure he's not some crazy evil sorceress. You decide to open a pop-up to perform that re-authentication (and, agreed, a modal window is probably the better choice here as well, but we'll run with it), you're going to want that pop-up to actually open.
Unfortunately, Mr. Public is running a fancy new-age browser that blocks pop-ups like an over-competitive dad at his kid's U-14 hockey game. He doesn't realize his browser is stopping him from performing this simple task, and the site isn't getting its reassurance that he's not a doppelganger.
The best response I've seen in this case is to stop everything and let Mr. Public know that
- His browser is too cool for school,
- The pop-up it's blocking isn't malware, and
- That you'd really like him to unblock this pop-up so he can go back to doing all the awesome stuff he wanted to do.
- Also, you'll probably want him to except your site from further nannying altogether so the mouse can also get his milk.
I would have it load a a page, in the site's normal livery (a.k.a. keep it in-brand), with a few simple sentences explaining the SNAFU and showing how to correct the interruption in the most popular browsers from which the site sees traffic.