Tendrías que hacer algo así:
$par = false
$query = mysql_query("SELECT * FROM tabla ORDER BY id DESC LIMIT 5");
while($query2 = mysql_fetch_array($query)) {
if ($par)
$bgcolor = "#FF0000";
else
$bgcolor = "#0000FF";
echo "<table><tr><td bgcolor='".$bgcolor."'>TEXTO..TEXTO</td></tr></table>";
$par = !$par;
}