Magento 1.9 – Creating Bundle Products with Fixed Items

This is just my opinion, so don't shoot if you don't like it.
I would use configurable products if the only configurable attribute is 'color'.
Pro
Using configurable products you take advantage of what Magento offers. Each product has it's own SKU, you can set out of stock only a few combinations, you can even make (custom) reports of how many red shirts you sold, and the list can go on.
Con
I know it can be a pain to manage them...but I assume you are not going to manage 1k products (* configurations) each day.

I would not take the custom options approach.
Pro
Maybe this has an advantage, because It can be easier to manage. You can even create an observer that will add the custom options on save so you won't have to add them manually. (here is how)

Conn You cannot set a combination out of stock.
Red for one product and Red for an other mean 2 different things.

I may take the bundle products approach by making each color a separate product, not visible individually.

Pro Can make an observer to add them on save so you don't have to add manually (I don't have a link for that).
Can manage prices for different combinations easier than for the configurable products.
Conn
Cannot make a combination out of stock unless all "red" combinations become out of stock.

This is what I got so far. I will add more as soon as I remember.

It is not possible with default settings on Product page in the Admin.

But you can customize the bundle/catalog/product/price.phtml to show the original price strikes.

<p class="old-price">
                    <span class="price-label"><?php echo $this->__('Regular Price:') ?></span>
                    <span class="price" id="old-price-<?php echo $this->getIdSuffix() ?>">
                        <?php                           
                        /** Changes - To show the regular price for Bundled Product **/
                        $_storeId = $_product->getStoreId();
                        $_store = $_product->getStore();
                        $_id = $_product->getId();
                        $_simplePricesTax = ($_taxHelper->displayPriceIncludingTax() || $_taxHelper->displayBothPrices());

                        $_convertedPrice = $_store->roundPrice($_store->convertPrice($_product->getPrice())); 
                        $_price = $_taxHelper->getPrice($_product, $_convertedPrice); 
                        $_regularPrice = $_taxHelper->getPrice($_product, $_convertedPrice, $_simplePricesTax); 
                        $_specialPriceStoreLabel = $this->getProductAttribute('special_price')->getStoreLabel();
                        /** Ends - To show the regular price for Bundled Product **/
                        echo $regular_formatted_price =  $_coreHelper->formatPrice($_regularPrice, false) ;
                        ?>

                    </span>
                </p>
                <p class="special-price">
                    <span class="price-label"><?php echo $_specialPriceStoreLabel ?></span>
                    <span class="price" id="product-price-<?php echo $_id ?><?php echo $this->getIdSuffix() ?>">
                    <?php echo $_coreHelper->currency($_minimalPriceTax) ?>
                    </span>
                </p>

I have uploaded the price.phtml here, please have a look and modify it based on your tax settings: https://github.com/svlega/Bundled-Price

This works for tax settings to show price including tax (without FPT).