This one: https://github.com/ethereum/pyethapp
and this one: https://github.com/ethereum/pyethereum
I have pyethapp running (the ipython console). What then is pyethereum?
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Pyethereum is the core blockchain related logic: transactions, blocks, contract VM, etc....
Pyethapp uses both pydevp2p for the p2p logic along with Pyethereum to create a complete Ethereum client.
So if you want a complete networked Ethereum client use Pyethapp. If you just want to experiment with the blockchain related logic you can use Pyethereum by itself.