It's unclear whether or not the shortage derives from stronger than expected demand for the handset, or if Apple didn't produce enough of that specific model in white. It doesn't seem to be the color that is driving the shortage. In the states where the 16GB white iPhone 3GS is in short supply, the $299 version with 32GB in white is well stocked. For example, in California 34 of the 45 stores have plenty of this unit in stock as do all 3 New York City locations. While many analysts had predicted shortages, no one expected a specific model to sell out well before the others.
Apple iPhone 3GS Specifications | Review