While WebCopy will download JavaScript enabled websites and detect any linked JavaScript in HTML tags, it does not parse and execute JavaScript, meaning it will not be able to fully download websites that use JavaScript to construct the page. Experimental JavaScript enabled-crawling can be enabled, but this has several caveats.
WebCopy only remaps links HTML and CSS, not JavaScript.
WebCopy does not download the raw source code of a web site, it can only download what the HTTP server returns. This means you cannot, for example, use WebCopy to download the PHP source code of a web site or any backend databases - unless that website is either badly configured or offers explicit source access via a normal download.
While WebCopy will do its best to create an offline copy of a website, data driven websites may not work as expected once they have been copied as the underlying source code and databases for a website can never be downloaded unless expressly offered by website owners.