NOTE: This suggestion is for JIRA Server. Using JIRA Cloud? See the corresponding suggestion.
JIRA should have an option to verify that a user owns the email address they claim to have, when signing up for an account.
Create dynamic groups - groups that automatically add users based on domain name of user's email address
Create an email verification for new customers created thought the Customer Portal.
JIRA 4.0 Enterprise Requirements
Allow default issue security level at user/users-group level
Captcha for new Account Signup
Disable Welcome E-Mail to New Customers
Validate email addresses of users who sign up
Confirm email address on activate account page