You can't save php since it runs ON THE SERVER.
You save html in files on your machine with no server.

> so for example if you have lines in the html like
> <link rel="shortcut icon"
> href="/wp-content/themes/alesca/favicon.ico"/>
> <link rel="stylesheet"
> href=http://alescavideo.com/wp-content/themes/alesc
> a/style.css" type="text/css" media="screen"/>
> <link rel="alternate" type="application/rss+xml"
> title="Wedding Video, Bar Mitzvah, Sweet 16 or any
> special occasion, Alesca Video Productions RSS Feed"
> href=http://alescavideo.com/feed/"/
> 
> then you could never use that site even if you had
> permission. YOU could copy the site yourself
> and edit it in a html editor cannot see the point of
> this software

Nothing above is php, it's html.  Httrack will get the html and related files
and change the links to relative file references. 

Your browser can then show the page without a internet connection.  That is
the point of the software.