I'd suggest reading http://macromates.com/blog/archives/2005/07/06/introduction-to-scopes/

As for comments, the Toggle Comment command in the Source bundle uses two variables (TM_COMMENT_START/END), these variables are set for misc. scopes (in the bundle editor), so even in an HTML file, it will use proper comment markers in the misc. <style>…</style>, <script>…</script>, <?php … ?>, <% # ruby %> etc. blocks -- and in plain HTML, it'll also work.

This however require that you have the language set to HTML (and not PHP, which would make the scope of the entire file source.php).