General: How It Works
JavaScript can be used client-side, or server-side but is mostly used on the client side, where it is an (X)HTML-embedded scripting language. An (X)HTML document can include any number of JavaScript scripts, which may be placed inline, in the header, or in a separate file.
PHP, like Perl, is a server-side technology. But also, this time like JavaScript, it is an (X)HTML-embedded scripting language. Before a requested page containing PHP code is sent from the server to the browser, the server invokes the PHP interpreter (external program or server module) to execute the embedded code and produce some (X)HTML code which is then sent to the browser along with the rest of the (non-PHP-produced) (X)HTML code on that page.
Perl is used on the server side for CGI (Common Gateway Interface) programming. Generally a separate script is run by the server to process data that has been sent from a browser. The script is run either by invoking a Perl interpreter which lives as a separate program on the server machine, or a Perl interpreter which is a module of the server program itself. The script may be in a single file or may include additional external files at execution time.