As a step in determining what happened to the bitcoin inside Mt. Gox, we have completed preliminary identification of the transfers of bitcoin on the blockchain which correspond to the transfers given in the leaked btc_xfer_report.csv file.
The algorithm used was able to identify a single corresponding transaction on the blockchain for 50% of deposits, corresponding to 77% of all bitcoin deposited at Mt. Gox since March 2011. For withdrawals, the algorithm identified 36% of transactions, corresponding to 75% of all bitcoin withdrawals over the same time period.
These identifications are the first steps in determining which bitcoin addresses may contain both hot and cold wallet storage of bitcoin for Mt. Gox. There is more work to be done, including using the identified transactions to trace internal flows of bitcoin based on the leaked Mt. Gox source code and identifying additional transactions to complete the record.
Further information is available at
http://www.reddit.com/r/mtgoxaddresses/wiki/transactionidentification. If you can assist this effort, please join us there.