Seriously. Physical access = No security. (DISCLAIMER: Assuming a stock configuration of Mac OS X) If a person with malicious intent can get physical access to your computer no amount of chmod'ding or obscure (available on Mac OS X) formatting is going to help you.

Rob is correct in suggesting the use of encrypted disk images. It's really the only way to go and it's what powers Mac OS X's filevault as well. Of course if the other person deletes the disk image you're done for either way.

But if we're talking about casual protection against a spouse deleting your important file then unchecking "Ignore permissions" should suffice.

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