My only concern was somthing you already laid to rest, and that would be the pop-up ads that can contain the hidden code. Not that they should work on me anyway, with NoScript running I hope I am reasonably safe from such things.
As for the rest then I really have no problem with anything you see fit to do. For the most part we are all here on your goodwill anyway and so can't see any attempt by you to get some revenue back in a bad light. The interstitial ads sound like they would indeed be the biggest ballache but the rest just sounds like any other site and who hasn't learned to live with those?
If you were to target specific areas with ads then I would guess the prime candidate would be the tutorial section? I would say that the forum least suited to adds would be the challenge forum, which would be nice kept clean of potential problems for people who are basically helping expand the site.