If you're running a full node - basically, Bitcoin-Qt or bitcoind - your client goes over every single transaction and verifies it as it is. In Bitcoin-Qt/bitco

If you're running a full node - basically, Bitcoin-Qt or bitcoind - your client goes over every single transaction and verifies it as it is. In Bitcoin-Qt/bitcoind, the client does not depend on transaction hashes to verify that a transaction took place, instead depending on the input/output lists. Any competently written "light" client does the same. Obelisk, written by the libbitcoin people, provides an address/transaction tracking system over the network that could be used if bitcoind does not meet requirements. Basically, this fix has been in place for a long time everywhere aside from MtGox.