It all depends on what you are doing, and what other measures you put into place.
storing files outside the public web tree - this is your best most secure method.
storing info in a mySQL database (using php files in a ssl directory) - this is second best, but can be just as good as the above as long as you secure your database properly.
storing files in a SSL directory - this isn't secure at all. Using SSL to transmit your sensitive data to/from the user is good, but you need to store it more securely that this.