In the question "Is there a way to prove ownership of a transaction?" the statement was made "A (regular) transaction must be signed with the private keys of the addresses of all the inputs".
Does that imply that a transaction has multiple signatures or is a single signature just encryted with multiple private keys?
Each input has its own and unique signature. This allows users to forge advanced transactions, such as offline signing where each participant agrees to provide inputs separately.
Even if all inputs belong to the same address, each one is signed separately (with the same private key in this case).
Oh, and multisignature addresses (P2SH, pay-to-script-hash) allow several signatures per input too!
