Magento 1.7 – How to Remove SKU Number from Order Email

Actually the piece of code does not create the order grid. This retrieves the ordered items for an order. It's used both in frontend and backend.

If you modify it to sort by sku then the items will be ordered by sku in the backend and frontend.
In order to do this you need to add this piece of code:

$this->_items->getSelect()->order('sku');

Right after

if ($nonChildrenOnly) {
    $this->_items->filterByParent();
}

Of course, don't edit the code. Override the model properly.
But I wouldn't recommend this approach. If you want the order of items by sku only in the backend you could sort them in the template.
The template is app\design\adminhtml\default\default\template\sales\order\view\items.phtml. You can replace the code that renders the items (I mean this):

<?php $_items = $this->getItemsCollection() ?>
    <?php $i=0;foreach ($_items as $_item):?>
        <?php if ($_item->getParentItem()) continue; else $i++;?>
        <tbody class="<?php echo $i%2?'even':'odd' ?>">
            <?php echo $this->getItemHtml($_item) ?>
            <?php echo $this->getItemExtraInfoHtml($_item) ?>
        </tbody>
    <?php endforeach; ?> 

With this:

<?php $_items = $this->getItemsCollection() ?>
    <?php $_sortedItems = array(); ?>
    <?php foreach ($_items as $_item) : ?>
        <?php $_sortedItems[$_item->getSku()] = $_item;?>
    <?php endforeach;?>
    <?php ksort($_sortedItems);//sort by sku?>
    <?php $i=0;foreach ($_sortedItems as $_item):?>
        <?php if ($_item->getParentItem()) continue; else $i++;?>
        <tbody class="<?php echo $i%2?'even':'odd' ?>">
            <?php echo $this->getItemHtml($_item) ?>
            <?php echo $this->getItemExtraInfoHtml($_item) ?>
        </tbody>
    <?php endforeach; ?> 

Again...don't modify the template. Put it in your own theme and modify it there.
Here is how you can change and admin theme.

Kudos for giving it a real shot!

Create a new module rewriting Mage_Sales_Model_Order_Pdf_Invoice. Copy/paste that model to your local module and remove any line that reads as follows:

$page->drawText(Mage::helper('sales')->__('Tax'), 480, $this->y, 'UTF-8');

You may have to reorganize the other totals as they're building up in a vertical column. Changing the value of the second parameter (480 above) in the other totals should be easy enough.

This solution will cover invoice PDFs. You were working in Abstract, which may suggest you want it removed everywhere. In that case, I would rewrite the other PDF implementations. They're all located in the same directory but with the names Creditmemo.php, Shipment.php.