<?php
$currentMenuId = JSite::getMenu()->getActive()->id ;

switch ($currentMenuId) {
    case 1:
		$color = "blue";
        break;
    case 2:
		$color = "red";
        break;
    case 3:
		$color = "green";
        break;
	default:
		$color = "yellow";
}
?>
<link rel="stylesheet" href="templates/your-template/css/<?php echo $color; ?>.css" type="text/css" />