You should do it in the grid template instead. You can add a new id to the order's row 'tr' . As an example, we'll highlight the orders placed in the last 24 hours.

Go to 
app/design/adminhtml/default/default/template/widget/grid.phtml. Starting in line 154: 

    ...
    <?php foreach ($this->getCollection() as $_index=>$_item): 
            $orderCreateAt = strtotime($_item->getCreatedAt());
            $last24hours = strtotime('24 hours ago'); ?>
            <tr id ="
            <?php if($orderCreateAt > $last24hours)
                { echo 'new-order'; }
            ?>"
            title="<?php echo $this->getRowUrl($_item) ?>"<?php if ($_class = $this->getRowClass($_item)):?> class="today <?php echo $_class; ?>"<?php endif;?> >
    ...

Now defying the style in css should be straightforward. 
Go to skin/adminhtml/default/default/boxes.css and add the style you'd like to have

    .grid table tr#new-order{
        background-color: #FF0000;
    }