Scenario:
You have set up google apps for your domain. Let the link be:- https://www.google.com/a/domain.com/

Now, you forgot the admin password.

Solution:
- Go to https://www.google.com/a/domain.com/ForgotAdminAccountInfo
- Submit the Captcha.
- The password reset instruction will be sent to the secondary email which you kept while creating the google app for your site.

That’s all. Hope this helps.