your best bet is to use event tracking...
http://code.google.com/apis/analytic...ckerGuide.html
something like this, inside of the google analytics code in your header should work.
PHP Code:
<?php if($_GET['mode'] = "search" && $_GET['q'] != ""){ ?>
_gaq.push(['_trackEvent', 'Site Search', '<?php echo $_GET['q'] ?>');
<?php } ?>
^ debug this, never ran it. oh and sanitize the inputs.
or you can opt to not mod_rewrite search queries... which is the easy fix.