Magento – Add a custom field per store view

In your payment model, you should set protected $_formBlockType = 'foo/form'; class that derives from Mage_Payment_Model_Method_Cc and create a template/foo/form.phtml file. This allows you to write your own form file.

Then you need to override assignData($data) function (payment model) in order to save this extra field value in the $paymentInfo obj.

In case you will need to show that field in info as well you can do the same as above with $_infoBlockType variable.

You can see here an explanation on how to add an extra field when editing a store view. You can do the same for websites and stores.
It involves adding a new column to the store view table and rewriting the admin block so you can add the field.
But I recommend you not to do that.
At least for websites and store views you can use the system->configuration section to add your fields. Alan Storm explains it here nicely how it works and how you can add your configurations and how you can read the values from config.