Adding a comment to an event during registration
You could setup a custom field for participants of the event (not contacts, nor the event, but the registration itself; Civi differentiates between contacts and participants; the registration entity is called 'Participants').

When creating the Custom Field Set, the "Used For" field would be for Participants (again, this is different from Contact).  Then when you add the field to the Profile you are going to use, the first dropdown for Field Name would be Participants; the second dropdown would be the custom field you just created.

Done this way, the Notes custom field you created only appears in the registration information (if you View the registration under a contact's Event tab), not in the Contact's Notes tab.

More details here: http://book.civicrm.org/user/events/setup/

Regarding the token for the confirmation email, because the custom field is for the registration/participant entity and not the contact entity, I think you will have to create a custom Token to access that data in the email template.