Both sites have temporarily pulled all their advertising in protest of these types of ads. And when the ads do come back, they'll be using direct ad sales only for a time, bypassing the big ad networks that were causing the problems in the first place, until the networks sort out their problems. There are two ways sites get advertising: another site emails them and asks to buy ad space (direct sales), and then they fill the rest of their space with ads from a network like Google AdSense (these are called remnant ads, since they fill the remaining space).
Wowhead and Thottbot were already telling the ad networks "don't show us these sorts of annoying ads," but the ad networks were doing their best to get around those restrictions. Cutting the networks out of the loop temporarily prevents them from making any money off Wowhead or Thottbot until they get their issues sorted out. It also prevents Wowhead and Thottbot from making any money from the ad networks, and as direct ad sales only account for a small part of the sites' revenue, this is not going to be sustainable in the long run.
Basically, they're taking a hit for the users here. Wowhead spokesperson Malgayne puts it as follows: "If our users have to see ads, I want them to at least be high quality ads." Ideally, the networks will get the message to stop putting up banners that flash, jiggle, beep, or pretend to be dialogue boxes, and everyone will get along happily again soon.