I expect to see more of these sorts of creative things. Advertising debt is annoying. And sadly people like PA with their 2 ads get nailed because people have been so massively inundated with ads all day that even one more is painful.
Another experiment they haven't tried, but would be good to run, would be to make the site subscriber only with the long tail free. So imagine a site where if you subscribed it was ad free and every few days you got a new comic. There is the 'free' site which is content that is a year old and has advertising on it, and there is a totally free site which has the two years old or later and its got no ads on it.
Of course its not as useful for topical content but its an interesting experiment.
Unfortunately for PA, their content is probably 90% games/pop culture topical. After a month it'd be completely stale and irrelevant (with exceptions of course).
I think the better move would be to have pay users not have to see any ads. Simple web re-design to remove that for pay users, otherwise free users still have to look at the ads. There are a ton of sites that do this and are quite successful.
I recently went through the comics archive from about 2004 until now. The comics still resonated, and I found myself frequently checking the blog posts to see what Tycho had said that day. While it was often about old events, it certainly wasn't stale or irrelevant to me.
Their goal is to redirect the people they have handling advertisers into projects for creating new content. Also, Mike tweeted (http://twitter.com/cwgabriel/status/222718794798350336) "I don't want to spoil some of the un-lockables but if we aren't making projects for advertisers we are free to make projects for you."
They clearly want to stop spending effort on ads altogether and spend it on new content for their readers, instead.
What's a site that only offers "no ads" as their paid-upgrade benefit? I haven't seen one offer just that, it usually comes with a grab-bag of other features that can't be replaced with a client-side script/extension. (DeviantArt's premium account is the upgrade I thought of. (http://sta.sh/047k5sokcr2) The two major client-side features of no ads and more thumbnails are solved with NoScript and AutoPager respectively.)
Off the top of my head, Wowhead offers an ad-free version for premium customers. I guess you also get custom forum avatars for being a premium customer.
The point is, free site that is ad-supported but those go away with a membership - whether you get extras or not.
The Facebook version of Words With Friends sells a 'no-ads' premium pack, but admittedly that's a bit of a different scenario as the ads are in-game modal dialogs that can only be dismissed after X seconds.
Back when I read PA I remember them saying that they were careful about who they let advertise on their site. Seeing a game advertised there was almost a tacit endorsement of it, and I'm not really sure removing those ads is in the readers' interest.
Aside from Google searches when I actually wanted to buy things, Penny Arcade had the only ads I ever looked at with actual interest.
(There's also the fact that if anyone is seriously bothered by the ads they're probably already blocking them themselves. I think people donating here are doing it to "give back", not because they actually care about the advertising.)
Judging by everything I have read, listened to, and watched of them over the past decade, I think they would have zero interest in any model where people only get content if they pay.
I expect to see more of these sorts of creative things. Advertising debt is annoying. And sadly people like PA with their 2 ads get nailed because people have been so massively inundated with ads all day that even one more is painful.
Another experiment they haven't tried, but would be good to run, would be to make the site subscriber only with the long tail free. So imagine a site where if you subscribed it was ad free and every few days you got a new comic. There is the 'free' site which is content that is a year old and has advertising on it, and there is a totally free site which has the two years old or later and its got no ads on it.
Of course its not as useful for topical content but its an interesting experiment.