How to add jQuery data in a table?

Note that in both cases, I used subtotal2 as a reference, but the logic is for any field. I also removed the short PHP tags ( <?= ) since they are not portable, but it is a mere suggestion. The formatting of the fields in monetary format with two houses is in charge of adjustments in the adopted solution (and already it escapes a lot of the scope).

With JQuery:

// Código principal:
$(function() {
    var soma = 0;
    $( ".subtotal2" ).each( function() {
        soma += Number( $( this ).html() );
    } );
    $( "#resultado" ).text( "R$ " + soma );
} );

<!-- Trecho HTML para demonstração: -->
<script src="https://ajax.googleapis.com/ajax/libs/jquery/2.0.0/jquery.min.js"></script><table><trclass="somatoria">
        <td>Balao de borracha</td>
        <td>12789</td>
        <td>R$ <span class="subtotal1">29.00</span></td>
        <td>1</td>
        <td>R$ 2</td>
        <td>R$ <span class="subtotal2">31.00</span></td>
    </tr>
    <tr class="somatoria">
        <td>CD Maria do Relento</td>
        <td>23419</td>
        <td>R$ <span class="subtotal1">33.00</span></td>
        <td>1</td>
        <td>R$ 0</td>
        <td>R$ <span class="subtotal2">33.00</span></td>
    </tr>
    <tr>
        <td colspan="5">TOTAL</td>
        <td id="resultado">?</td>
    </tr>
</table>

With PHP:

<?php
    $soma = 0;
    while($M_P = mysql_fetch_array($Dados_Produtos)) {
        $subtotal2 = $M_P['preco'] * $M_P['quantidade'] + $M_P['taxas'];
        $soma += $subtotal2;
?>
    <tr class="somatoria">
        <td><?php echo utf8_encode($M_P['produto']); ?></td>
        <td><?php echo $M_P['codigo']; ?></td>
        <td>R$ <span class="subtotal1"><?php echo $M_P['preco']; ?></span></td>
        <td><?php echo $M_P['quantidade']; ?></td>
        <td>R$ <?php echo $M_P['taxas']; ?></td>
        <td>R$ <span class="subtotal2"><?php echo $subtotal2; ?></span></td>
    </tr>
<?php } ?>
    <tr>
        <td colspan="5"></td>
        <td>R$ <?php echo $soma; ?></td>

You can use .reduce ()

// criar uma array com os valores
var subTotais = $('.subtotal1').map(function () {
    return parseFloat(this.innerHTML);
}).get();
// somar todos
var total = subTotais.reduce(function (a, b) {
    return a + b;
});
// exibir resultado
console.log(total); // resultado

var totais = $('.subtotal1').map(function () {
    return parseFloat(this.innerHTML);
}).get();
var total = totais.reduce(function (a, b) {
    return a + b;
});
alert(total); // resultado

<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.11.1/jquery.min.js"></script><table><trclass="somatoria">
        <td>
            <?=utf8_encode($M_P[ 'produto'])?>
        </td>
        <td>
            <?=$M_P[ 'codigo']?>
        </td>
        <td>R$ <span class="subtotal1">29.00</span>

        </td>
        <td>
            <?=$M_P[ 'quantidade']?>
        </td>
        <td>R$
            <?=$M_P[ 'taxas']?>
        </td>
        <td>R$ <span class="subtotal2">29.00</span>

        </td>
    </tr>
    <tr class="somatoria">
        <td>
            <?=utf8_encode($M_P[ 'produto'])?>
        </td>
        <td>
            <?=$M_P[ 'codigo']?>
        </td>
        <td>R$ <span class="subtotal1">29.00</span>

        </td>
        <td>
            <?=$M_P[ 'quantidade']?>
        </td>
        <td>R$
            <?=$M_P[ 'taxas']?>
        </td>
        <td>R$ <span class="subtotal2">29.00</span>

        </td>
    </tr>
</table>