When you make a deposit you are extending credit. In the case of Mt. Gox, or any other Bitcoin exchange, that credit is secured by nothing and insured by noöne.
Advice, going forward, for managing counterparty risk:
(1) Split a $100 transaction into 10 $10* transactions executed incrementally (send $10 of BTC to Mt. Gox, exchange it, transfer it out, and only then send the next $10 of BTC over). This keeps exposure at any given time at a manageable level. The downside is it increases exposure to BTC/USD volatility.
(2) Split a $100 into 5 $20 transactions executed simultaneously on many exchanges. This keeps exposure to any single institution at a manageable level. The downside is it increases the number of institutions which must be dealt with.
(3) Draft a special arrangement with the institution for a large transaction. This should include credit and speedy withdrawal guarantees. The downside is the legal cost.
*edit: I am illustrating a hypothetical $100 transaction. Substitute, in place of $10, the most you are willing to lose in the event the exchange proves insolvent.
Advice, going forward, for managing counterparty risk:
(1) Split a $100 transaction into 10 $10* transactions executed incrementally (send $10 of BTC to Mt. Gox, exchange it, transfer it out, and only then send the next $10 of BTC over). This keeps exposure at any given time at a manageable level. The downside is it increases exposure to BTC/USD volatility.
(2) Split a $100 into 5 $20 transactions executed simultaneously on many exchanges. This keeps exposure to any single institution at a manageable level. The downside is it increases the number of institutions which must be dealt with.
(3) Draft a special arrangement with the institution for a large transaction. This should include credit and speedy withdrawal guarantees. The downside is the legal cost.
*edit: I am illustrating a hypothetical $100 transaction. Substitute, in place of $10, the most you are willing to lose in the event the exchange proves insolvent.