I don't think in-text advertising is leaving us anytime soon. So, I think the best thing you can do is to make the difference between normal links and ad links very noticeable. The little pop-up should not be very large, slow to load, or look like it might be some type of legitimate information source. It should totally say in big letters at the top: "Advertising by SeatGeek." Black background, white bold text.
I've thought about this a couple times, trying to see if I could come up with something that the established companies haven't. I really can't wait for some clever person to figure out the perfect way to put in-text ads in content.
Maybe there should be no ad links at all, but a little icon to the right of the phrase, that upon mouseover will highlight the phrase and display the pop-up.
Ultimately though this method of advertising gives site owners the opportunity to deceive their visitors into clicking ad links. Less so than Adsense, I would think.
--- Edits for proof reading