I'd steer clear of javascript. As the article points out, many people surf with it turned off (myself included) to limit the damage a hostile web site can do to their computers.

CGI also has problems: poorly designed code can open security holes on the server. Hosts tend to frown on that sort of thing, so CGI access is not generally granted unless you beg for it and can present a reasonable need for it.

I use CSS to manage my layouts and a utility with global find/replace whenever I need to make an update to navigation. Notepad++ was the one I used most recently. Not the most elegant way to go about it, but it's suitable for someone with my limited understanding of PHP. Someday I'll bone up on more dynamic solutions, but for now my manual approach is working okay.