Te faltava comprobar que res1 y res2 fuera mayor que 0 antes de imprimir el resultado en el campo total... sino escribe NaN i tendrias que haberlo puesto en blanco antes de volver a escribir.
ahora ya va.
Código:
<html>
<head>
<title>Ensayo</title>
<SCRIPT>
function calculate(){
var val1,val2,valsub,sumar,restar,res1,res2;
val1 = ((document.calcform.price1.value)*(document.calcform.quantity1.value));
val2 = ((document.calcform.price2.value)*(document.calcform.quantity2.value));
valsub = ((val1) + (val2));
document.calcform.subtotal.value = valsub;
sumar = parseInt(document.calcform.sumarle.value);
res1= ((valsub) + (sumar));
if(res1>0){
document.calcform.total.value = res1;
}
restar = parseInt(document.calcform.descuento.value);
res2= ((valsub) - (restar));
if(res2>0){
document.calcform.total.value = res2;
}
}
</SCRIPT>
</head>
<body onload="document.calcform.price1.focus();">
<FORM name="calcform">
<table width="80%" border="0" align="center">
<tr>
<td><TABLE width="50%" border=0 align="center" class="Yuyo" >
<TR>
<TD width="32%"><center>Valor </center></TD>
<TD width="32%"><center>Cantidad</center></TD>
</TR>
<TR>
<TD><INPUT type="text" name="price1" ONCHANGE="javascript:calculate();"></TD>
<TD><INPUT type="text" name="quantity1" ONCHANGE="javascript:calculate();"></TD>
</TR>
<TR>
<TD><INPUT type="text" name="price2" ONCHANGE="javascript:calculate();"></TD>
<TD><INPUT type="text" name="quantity2" ONCHANGE="javascript:calculate();"></TD>
</TR>
</TABLE>
<p> </p>
<table width="46%" border="0" align="center" class="Yuyo">
<tr>
<td><div align="right"></div></td>
<td colspan="2"><center>
</center></td>
</tr>
<tr>
<td><div align="right">Subtotal</div></td>
<td colspan="2"><center>
<INPUT type="text" name="subtotal" >
</center></td>
</tr>
<tr>
<td><div align="right">Sumarle:</div></td>
<td colspan="2"><center>
<input type="text" name="sumarle">
</center></td>
</tr>
<tr>
<td><div align="right">Restarle:</div></td>
<td colspan="2"><center>
<input type="text" name="descuento" >
</center></td>
</tr>
<tr>
<td><div align="right">Total:</div></td>
<td colspan="2"><center>
<INPUT type="text" name="total">
</center></td>
</tr>
<tr>
<td colspan="3"><center>
</center></td>
</tr>
<tr>
<td colspan="3"><center>
<INPUT name="button" type="button" ONCLICK="javascript:calculate();" Value="Calcular">
</center></td>
</tr>
<tr>
<td colspan="3"><div align="right"></div>
<center>
</center></td>
</tr>
</table>
<p> </p></td>
</tr>
</table>
</form>
</body>
</html>