wolfire is kind of an exception in that they don't use proper e-commerce service providers like fastspring, bmt-micro, plimus, etc. -- i'm not sure why they don't do that, but you probably shouldn't model yourself on them
Pay-what-you-want requires a payment processor that will not charge more than $0.01 for a $0.01 transaction. PayPal/Amazon Payments/Google Checkout don't as far as I know and they have the lowest minimum fees.
By the way, Sweden-based Mojang (Mincraft) uses PayPal and MoneyBookers but neither Amazon Payments nor Google Checkout.