Magento – Product price matrix

There are two extension which does this for you:

Simple Configurable Products

http://www.magentocommerce.com/magento-connect/simple-configurable-products.html

BCP - Better Configurable Products

http://www.magentocommerce.com/magento-connect/better-configurable-products.html

Here is how you can get the prices of the simple products. The example is for a single configurable product but you can integrate it in your loop.
There may be a problem with performance because there are a lot of foreach loops but at least you have a place to start. You can optimize later.

//the configurable product id
$productId = 126; 
//load the product - this may not be needed if you get the product from a collection with the prices loaded.
$product = Mage::getModel('catalog/product')->load($productId); 
//get all configurable attributes
$attributes = $product->getTypeInstance(true)->getConfigurableAttributes($product);
//array to keep the price differences for each attribute value
$pricesByAttributeValues = array();
//base price of the configurable product 
$basePrice = $product->getFinalPrice();
//loop through the attributes and get the price adjustments specified in the configurable product admin page
foreach ($attributes as $attribute){
    $prices = $attribute->getPrices();
    foreach ($prices as $price){
        if ($price['is_percent']){ //if the price is specified in percents
            $pricesByAttributeValues[$price['value_index']] = (float)$price['pricing_value'] * $basePrice / 100;
        }
        else { //if the price is absolute value
            $pricesByAttributeValues[$price['value_index']] = (float)$price['pricing_value'];
        }
    }
}

//get all simple products
$simple = $product->getTypeInstance()->getUsedProducts();
//loop through the products
foreach ($simple as $sProduct){
    $totalPrice = $basePrice;
    //loop through the configurable attributes
    foreach ($attributes as $attribute){
        //get the value for a specific attribute for a simple product
        $value = $sProduct->getData($attribute->getProductAttribute()->getAttributeCode());
        //add the price adjustment to the total price of the simple product
        if (isset($pricesByAttributeValues[$value])){
            $totalPrice += $pricesByAttributeValues[$value];
        }
    }
    //in $totalPrice you should have now the price of the simple product
    //do what you want/need with it
}

The code above was tested on CE-1.7.0.2 with the Magento sample data for 1.6.0.0.
I tested on the product Zolof The Rock And Roll Destroyer: LOL Cat T-shirt and it seams to work. I get as results the same prices as I see in the frontend after configuring the product by Size and Color