The following answer refers exclusively to the SEPA transfers within the EU:
You may leave the SEPA Reference field empty. Consult your own bank on how this is done.
The most important point to successfully process your deposit with Bitstamp is the “Message”, generated in their Deposit form. You have to include this number in your bank deposit message so that Bitstamp will know this is your account. Please, refer to our detailed instructions in Depositing funds on your Bitstamp account.
For users outside of the EU: please, contact your own bank to find out how to correctly process your money transfer according to the data presented in Bitstamp’s deposit form.