Wherever Mt. Gox is storing people's bitcoins (the exchange's wallet.dat) and their deposits in USD and EUR, as well as wherever trades, deposits, and - especially - withdrawals are processed. Lots of people have large non-bitcoin deposits in the exchange, and if a raid on a small number of locations in Japan can prevent them from withdrawing or result in their money being seized, that's a serious issue for the bitcoin project as a whole.

Edit: Also, it looks like Mutum Sigillum LLC, the company that processes Mt. Gox's deposits and withdrawals through Dwolla, is incorporated in Delaware. I wonder if they process those transactions in the US?