User blog comment:Lancer1289/Wikia's New Skin, the countdown begins/@comment-1074875-20100928213440/@comment-2088100-20100928220555

As they mention further down in the blog, the ToU are only referring to site-wide CSS and JS, i.e. stuff that everyone who visits the site will see. You are free to modify your own personal CSS and JS to change the site however you like.