You'll want to define a toggle in the page script, and have the slideshow function only execute if the toggle is not set. Then link your menu item hover events to that toggle::
<script src="//ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js"></script>
<script type="text/javascript">
debugger;
var canSlide = true;
function slideShow() {
if(canSlide)
{
var showing = $('#slideshow a.show');
var next = showing.next().length ? showing.next() : showing.parent().children(':first');
var timer;
showing.fadeOut(800, function() { next.fadeIn(600).addClass('show'); }).removeClass('show');
}
setTimeout(slideShow, 5000);
}
$(document).ready(function() {
slideShow();
});
$(".menubar ul li ul li a").mouseover(function(){canSlide = false;}).mouseout(function(){canSlide=true;});
</script>