I have not looked that hard but I know can buy from Humble Bundle (For at least 2 years), Groupees, and Story Bundle. Amazon Payments, Google Wallet, and Paypal have a bit of a rivalry so anything connected to one will be unable to use the others. And Amazon has some limits on using Amazon Payments, for example no buying Amazon Prime and some digital goods are off limits too.
Edit: Just checked, and both current Humble Bundles are working with Amazon Payments. It did not show paying from balance as an option when you tried for higher than your balance. My most recent bundle purchases via Amazon were: E3 Digital Ticket, Humble Rebundle 8, and Weekly Sale: Double Fine.
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Are there any stores in which I can use my Amazon credit? I know I can buy HBs, but are there more stores?
Edit: Yes, I know that I can buy games from Amazon itself.
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