You know who has the worst intrusive popups? Stack Overflow. First, if you are logged in but haven't visited in a while. They put a position fixed huge bar on the top reminding you that you haven't been to the site in a while. I hated that popup.
They've done a lot of work on making it more annoying recently. The "continue" button that actually means "don't continue but instead go and install the app" is inspired-evil.
The flashing app icons, seemingly on every interaction, .. I mean for real.
I think the absolute worst is Imgur on mobile. They display a large modal that takes up 95% of your screen so you can't even view the image you were linked to. They don't even hint that you're opting in to something when clicking the big green button to dismiss. And instead of giving you a button saying you do not consent, they force you to uncheck hundreds of checkboxes across four different pages. I actually had to find a different image host because I don't want to subject more people to imgur.
