I think it's because needs evolved. When we went away from tables to use stylesheets, the goal was to keep the same html but alter the presentation with css and js (for the animations). But now, it's not just about presentation anymore. Real applications are built and maybe it doesn't make sense to keep the html and throwing away css/javascript on a full-rewrite. Basically, the html we code right now is way more tied to the javascript that it once was. So, having them in two separate files doesn't make that much sense.

Oh, and, you can use $('#show-help-link').click(showHelp); instead of click(function() { showHelp(); }); ! : )