The Bitcoind daemon is spending unconfirmed outputs as inputs in new transactions. This is leading to dependency chains that could be susceptible to double spends.
Some examples of this behavior:
This transaction https://blockchain.info/tx/35c4e8c86075cf3f5335e029abd2d981af011c142b56e04c0a6d8b0d588d32ae which included a fee spent the unconfirmed output transaction https://blockchain.info/tx/99e6c22980571d1733986d950f564854393777ba0905d08aae36d7f4f64e4a3a which included no fee.
Note that in both cases, the only command executed against the Bitcoin Daemon (0.8.5) was "sendtoaddress". Also note that https://blockchain.info/tx/35c4e8c86075cf3f5335e029abd2d981af011c142b56e04c0a6d8b0d588d32ae had to have its raw tx manually pushed using blockchain.info/pushtx functionality in order to appear. This is what led to the discovery that unconfirmed outputs were being spent.
This issue appears to have become noticeable because of the increased user traffic on the Bitcoin network leading to more transactions with no fees. As a consequence, miners are cherry picking transactions with fees leading to backlogs and dependency chains becoming evident. There are numerous issues in the bitcointalk.org [Technical Support] sub-board as well as topics such as: https://bitcointalk.org/index.php?topic=339792.0 on the problem.