hola
para obtener los valores de los campos es mejor ponerlos dentro de un form y ademas te faltan el cierre de las comillas dobles en maxlength=\"5\
<script language=javascript>
function Sumar()
{
var n1 = new Number(form.n1valor.value) ;
var n2 = new Number(form.n2valor.value) ;
var n3 = new Number(form.n3valor.value) ;
v = n1 + n2 + n3;
form.total.value=v ;
}
</script>
<form name="form" method="post" action="">
<?
echo "<table width=\"423\" border=\"0\">";
echo "<tr>"
."<td width=\"89\"><span class=\"boxtext\">Seguridad</td>"
// ."<td colspan=\"89\">Seguridad</td>"
."<td width=\"56\"><span class=\"boxtext\"><input name=\"n1valor\" type=\"text\" size=\"5\" maxlength=\"5\" onChange=\"Sumar()\">"
."%</td>"
."<td width=\"120\"><span class=\"boxtext\"> </td>"
."<td width=\"140\"><span class=\"boxtext\"> </td>"
."</tr>"
."<tr>"
."<td><span class=\"boxtext\">Operación</td>"
."<td><span class=\"boxtext\"><input name=\"n2valor\" type=\"text\" size=\"5\" maxlength=\"5\" onChange=\"Sumar()\">"
."%</td>"
."<td> </td>"
."<td> </td>"
."</tr>"
."<tr>"
."<td><span class=\"boxtext\">Mecanica</td>"
."<td><span class=\"boxtext\"><input name=\"n3valor\" type=\"text\" size=\"5\" maxlength=\"5\" onChange=\"Sumar()\">"
."%</td>"
."<td> </td>"
."<td> </td>"
."</tr>"
."<tr>"
."<td> </td>"
."<td> </td>"
."<td> </td>"
."<td> </td>"
."</tr>"
."<tr>"
."<td><span class=\"boxtext\">Resumen</td>"
."<td colspan=\"2\"><input name=\"total\" id=\"total\" type=\"text\" readonly size=\"30\" maxlength=\"30\"></td>"
."<td> </td>"
."</tr>"
."<tr>"
."<td> </td>"
."<td> </td>"
."<td> </td>"
."<td> </td>"
."</tr>";
echo "</table>";
?>
</form>