Magento Product Quantity Uses Decimals – How to Manage

You may want to take a look at getBuyRequest in app/code/core/Mage/Sales/Model/Quote/Item.php.

This method appears to be used to pull the product options, and then add them to the quote.

However, you would also want to modify the setProduct method as well, so that way you can setQty() on the Product being saved to the model to reference later in buyRequest.

You could do something like:

->setQty(Mage::getModel('cataloginventory/stock_item')->loadByProduct($product)->getQty())

in setProduct().

I wouldn't recommend doing these things in app/code/local/Mage overrides though, it would definitely be better to create a module for these things. In fact, you could accomplish this through an Observer event, listening for sales_quote_item_save_before and do something similar to:

public function checkQuoteItemQty($obs) {
    $event = $obs->getEvent();
    $item = $event->getDataObject();

    $product = Mage::getModel('catalog/product')->load($item->getProduct()->getProductId());
    $itemInventory = Mage::getModel('cataloginventory/stock_item')->loadByProduct($product);

    if ($item->getQty() > $itemInventory->getQty()) {
        $item->setQty($itemInventory->getQty());
    }

    return $this;
}

Hope this helps!

This happens because the configurable product does not have minimum sale qty and a total qty.
You need to get the simple product that is represented by the configurable product and get the values from it. Try this:

$simpleProduct = null;
foreach ($_item->getQuote()->getAllItems() as $simpleItem){
   if ($simpleItem->getParentId() == $_item->getId()){
       $simpleProduct = $simpleItem->getProduct();
       break;
   }
}
if ($simpleProduct){
   //work your magic with $simpleProduct
}

I didn't test, but it seams like the way to go.
I've tested and this works for me. I was close. Instead of getParentId() it should be getParentItemId(). Here is the code from my checkout/cart/item/default.phtml file:

$simpleProduct = $this->getProduct();
if ($this->getProduct()->getTypeId() == 'configurable') {
    foreach ($_item->getQuote()->getAllItems() as $simpleItem){
        if ($simpleItem->getParentItemId() == $_item->getId()){
            $simpleProduct = $simpleItem->getProduct();
            break;
        }
    }
}
$stockItem = Mage::getModel('cataloginventory/stock_item')->loadByProduct($simpleProduct);
$min_sale_qty = (int)$stockItem->getData('min_sale_qty');
$total_qyt = (int)$stockItem->getQty();

?>
<select name="cart[<?php echo $_item->getId() ?>][qty]">
    <?php for($i = $min_sale_qty; $i <= $total_qyt; $i = $i + $min_sale_qty) : ?>
        <option value="<?php echo $i?>" <?php echo ($i == $this->getQty())? "selected=selected": ""; ?>>
            <?php echo $i?>
        </option>
    <?php endfor;?>
</select>

I'm almost sure that there is an other way of getting the simple product and avoid the foreach loop but this will do for now.