Reddit does well at unobtrusive ads. Their sidebar ads are easily blocked by adblock, and occasionally they'll just run an ad with a happy reddit alien saying "thank you for not using adblock!" -- a lot of reddit users have their adblock settings set specifically to allow ads from reddit, in order to support the site.

ETA: I suspect the ad would be closed less often if there were a note nearby naming the specific charity to which that ad was providing revenue.