PHP doesn't parse files with a .js
ending, but you could have the PHP parser parse javascript files, but that's a really bad idea, instead insert the PHP in the PHP file where it belongs, and get the data with javascript
<div id="some_element" data-startingslide="<?php echo $_GET["thumb"] ?>"></div>
then do
var startingSlide = $('#some_element').data('startingslide')
$(slideshowContainer).cycle ({
startingSlide: startingSlide
});