I've turned the preliminary payment protocol spec into three BIPs:

https://en.bitcoin.it/wiki/BIP_0070 : Network protocol / messages
https://en.bitcoin.it/wiki/BIP_0071 : MIME types for the messages
https://en.bitcoin.it/wiki/BIP_0072 : bitcoin: URI extension

I expect the wallet-side implementation to be pulled into Bitcoin-Qt Real
Soon:
  https://github.com/bitcoin/bitcoin/pull/2539

There is also a reference implementation of server-side code for generating
payment requests in php and C++ :
  https://github.com/gavinandresen/paymentrequest

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Gavin Andresen