* Legal fees for sending a couple of threating letters.
What have they gained?
* A full-page spread in The Oatmeal advertising the fact to all readers of Slashdot, HN, and many other social media sites that Funnyjunk exists, carries user-submitted comics such as would be interesting to readers of The Oatmeal, and are friendlier to content submitters than they are to the DMCA.
* Massive SEO links. Four out of the first six search results for "the oatmeal" from DDG refer to Funnyjunk. Funnyjunk has an entire section on http://en.wikipedia.org/wiki/The_Oatmeal#FunnyJunk_legal_dis... and an entire article dedicated to the dispute.
Now most of us want to believe "But this is negative publicity and Funnyjunk couldn't possibly want that". But before you conclude that, consider how little people are going to remember about this incident in just a few weeks. For example, do you remember even today the name of the Funnyjunk CEO or of his lawyer? I don't, but I remember Funnyjunk whereas I had never heard of it at all before. I've even been to their site several times now (following up on links posted at The Oatmeal).
I hate to say it, but this was brilliant and The Oatmeal fell for it.