It is better to just avoid JavaScript in the body all together. It makes things easier to update, avoids the needs for comments and forces you to plan for non-JavaScript enabled users as well as users with JavaScript enabled.
HTML comments, ie. <!-- -->, are no longer needed. They were intended to allow browsers that didn't understand the <script> tag to degrade gracefully. These browsers, eg. Netscape 1.x are no longer found in the wild. So there is really no point in putting HTML comments in your script tags anymore.
If you want your HTML to validate as XHTML or XML, you probably want to use a commented out CDATA tag.
The reason for this is so your <, >, &, " and ' that are part of your javascript code won't have to be encoded as <, >, &, " and ' respectively.
..the difference with yours being that a rare obscure browser that may not understand the script tag will print the opening // to the screen, which kind of defeats the purpose of putting the comment tag there in the first place.
However in the end even super obscure browsers that don't support javascript by default (like HTMLLayout browse or Netsurf) know it is best not to render the text between script tags, so no, it is no longer relevant by any means. However all browsers you could possibly care about understand the <!-- syntax, so there is no real need to madly worry about removing it from what you already have, because it is valid js, just remember to not add it next time.
Even in modern browsers, it can be useful. I actually ran into this problem today, precisely because I wanted to avoid having javascript embedded in my html.
I have an html page that is served up on http://host/variable_app_name/pagename, where variable_app_name can have many values (y'know, variable). If it wants to access static files it has to use a url like http://host/static/variable_app_name/filename, so I cannot specify the static file location without first looking at browser's location to find the value of variable_app_name.
To link to the main javascript file I do the following:
The above code will explode even in the latest version of Chrome, because the script tag will be terminated in the middle of a javascript string and the remainder of the string will be interpreted as html, like so: