One comic I'm glad hasn't been mentioned is Order of the Stick. That stands far too well in its webcomic format that I think any adaptation would lose a lot of its charm.
I think a lot of writers could learn something from OotS about how to have villains with diverse and nuanced motivations, but you're right, I don't think that it works in any other medium. Adapting the visual style to motion would become a gimmick that is all too likely to overstay it's welcome, and even if you wanted to just throw out the entire title, too much of the world and the characters rely on meta-references that are aimed at a niche audience. Order of the Stick is not something I'd try to sell to someone who has no interest in D&D.
I had similar reasons for not mentioning Megatokyo. There's just too many in-jokes that aren't just throw-away gags, but actual world-building. I think a movie would either have throw out too much of what makes Megatokyo what it is, or it would spend too much time explaining the world to the audience. Not to mention that Megatokyo is just kind of floundering, with nowhere near the active fanbase it once had.
Which brings to mind a number of other comics that I didn't mention because they're either finished, abandoned, or otherwise inactive:
- Applegeeks : I really love the character of Eve, and I'm still sad that most of her story never made it into print.
- Finders Keepers : a little too reminiscent of Neverwhere, in some aspects, but still a fantastic story
- The Grand Blue Door : I think this comic is completely vanished from the web, but it was like Anne of Green Gables meets D&D. Seriously, I want more of this. Give me fantasy versions of other genres.
- Angels 2200 - because, duh.
- Cascadia - another webcomic that has pretty much completely vanished. This one had amazing art. It already looked like stills from an animated movie, and the story was pretty good too.