http://www.proofofexistence.com/about -- "Use our service to anonymously and securely store an online distributed proof of existence for any document."
The document is certified via embedding its SHA256 digest in the bitcoin blockchain. This is done by generating a special bitcoin transaction that encodes/contains the hash via an OP_RETURN script. This is a bitcoin scripting opcode that marks the transaction output as provably unspendable and allows a small amount of data to be inserted, which in our case is the document's hash, plus a marker to identify all of our transactions.
Naïve question perhaps, but if the bitcoins are lost forever, this seems like an unfriendly use of the bitcoin protocol and the blockchain, and future versions of the protocol may prevent this type of transaction from being accepted into the blockchain?