Just do a test for it, of course:
while ($row = mysql_fetch_array($equipresult))
{
extract($row);
$onhand = $receivedsum - $shippedsum;
echo "<table border=1 width=70% cellpadding=1 cellspacing=1 align=center>";
echo "<tr>
<td width=35%><font size='2'>$item</font></td>
<td width=8%><font size='2'>$shippedsum</font></td>
<td width=8%><font size='2'>$receivedsum</font></td>
<td width=8%><font size='2'";
if ($onhand <= 0)
echo " color='red'";
echo ">$onhand</font></td>
</tr>";
btw, you might want to consider using CSS instead of the deprecated <font> tag.