Wordpress can get pretty grimey in the head, droppin in all kinds of nasty bits. So, I always include a cleanup.php deal (included within functions.php), with a bunch of functions to tidy up the nav, body class, lang, js and css outputs, et cetera, et cetera. Here's the Mr. Clean treatment for js and css output. Of course, remember to prefix boss.

Wordpress Cleanups for JS and CSS

<?php

/*-----------------------------------------------------------------------------------*/
/*  Clean them stylesheet <link> tags
/*-----------------------------------------------------------------------------------*/ 
function clean_style_tag($input) {
  preg_match_all("!<link rel='stylesheet'\s?(id='[^']+')?\s+href='(.*)' type='text/css' media='(.*)' />!", $input, $matches);
  // Display media if it's print
  $media = $matches[3][0] === 'print' ? ' media="print"' : '';
  return '<link rel="stylesheet" href="' . $matches[2][0] . '"' . $media . '>' . "\n";
}

add_filter('style_loader_tag', 'clean_style_tag');

/*-----------------------------------------------------------------------------------*/
/*  Remove versions from css/js while we're at it
/*-----------------------------------------------------------------------------------*/ 
function remove_cssjs_ver( $src ) {
    if( strpos( $src, '?ver=' ) )
        $src = remove_query_arg( 'ver', $src );
    return $src;
}
add_filter( 'style_loader_src', 'remove_cssjs_ver', 1000 );
add_filter( 'script_loader_src', 'remove_cssjs_ver', 1000 );

?>