I agree with you on the really intrusive ads...they are the reason why I (and most blockers, I believe) started blocking in the first place. But realistically, that's not something Ars puts up with from their advertisers. They really do work hard to keep a very clean, non-intrusive website.
They're one of the few I have whitelisted, along with BluesNews. And in all honesty, Ars is better about keeping their ads minimal. But BluesNews has ads that I'm more likely to be interested in (better targeting)...so those two show both of the approaches that are likely to get -my- eyes.