Girl Genius is the one I'd be excited for.
I suppose Mega Tokyo has a shot, isn't it already published in Japan or something?
Probably not anime, but Digger is something I want to see animated. It has the advantage of being finished, too, and probably would be 12 or 24 episodes in total, which fits my preferences. Second and third choices would be Gunnerkrigg Court and Girl Genius, I suppose.
You will not go to space today.Dark Legacy. The break between the art styles of the actual comic and any anime adaptation would be hilarious to watch.
And this is the actual XKCD poster, if you don't want to do a lot of clicking.
http://www.cracked.com/photoplasty_143_if-every-website-got-dramatic-movie-adaptation_p19/#15
edited 8th Dec '12 10:45:20 AM by TamH70
Ahahahaha, oh Lord, there's TV Tropes at the end of that list. And it looks like they just ripped the picture of The Expendables or something similar.
Anyway. El Goonish Shive seems appropriate. But maybe that has more of an American cartoon aesthetic.
I would love to see an archer-styled adaptation of Questionable Content.
Go play Kentucky Route Zero. Now.Not anime, but I second animated Digger and Paranatural. Archipelago would lend itself well to an episodic format, too.
Dopants: He meant what he said and he said what he meant, a Ninety is faithful 100%.Part of the problem is that many webcomics have a distinctly Western setting, even with their art styles. So, while I hate to pop bubbles, it's likely the best you could probably hope for most cases would be a anime-style adaptation done by a Western studio.
edited 8th Dec '12 7:06:58 PM by TotemicHero
Expergiscēre cras, medior quam hodie. (Awaken tomorrow, better than today.)I don't see that as a less good thing to hope for, as long as it's a good studio.
I think City Of Reality would be a good candidate for animation. The comic has sort of taken a half step in that direction already.
edited 8th Dec '12 11:28:31 PM by Desertopa
...eventually, we will reach a maximum entropy state where nobody has their own socks or underwear, or knows who to ask to get them back.^ Exception: The webcomic source in question has been subject to significant Art Evolution.

I know it's silly, but there are some webcomics that are written in a manga way. Imagine what it be like if there's one webcomic that gets an anime adaptation.
If The Magnificent Milkmaid gets one, I could think of this: