Is it possible to use SSI to add in some code for javascript head tags.. I want to hide them because the javascript is to display hidden links, and I don't need people snooping around the source code.

Make a Perl script that checks the password, or cookie, or whatever instead of JavaScript, and if the user has permission it shows it, if not it doesn't, then call it in exec cgi.

Well, I was going to use PHP, but I haven't coded the site yet, but I still need a hidden link and need to be able to hide it.