Board Thread:General Discussion/@comment-16804948-20140408204016/@comment-1330470-20140409072136

Wikia engineers did it by editing PHP files, I guess. I don't know a whole lot about that. The new look went public from October to November of 2010. (Prior to that, there was a different Wikia-custom skin used on the site, called Monaco).

As for why, well, Archive:Wikia's_new_look_-_FAQ gives a few reasons why Wikia did it - I personally will always prefer the Monobook skin though.