It's funny how many JS-related projects choose nondescript names like this. Off the top of my head: "processing", "underscore", "node", "backbone", "mylibrary", and (maybe the one that started it all) "prototype". I caught myself doing it after I named one of my js libraries "coordinate".
I'm not suggesting "three.js" is a bad name--it's simple, and I'll probably remember it. It's just an interesting naming trend.