This tutorial provides instruction to allow Google Apps users to choose their own theme for GMail. Google Apps users by default do not have the required permission to select a theme in GMail. But as a Google Apps administrator you can enable the users to choose their own theme . And this featured can be enabled via Email Settings.
Login to your Google Apps account as an administrator. Navigate to General tab under the Email Settings.
In Email General Settings page, scroll down to Themes section and tick the check box with label as Let users choose their own themes. Click the Save changes button to confirm and save the changes.
This would display the Themes tab on user’s Mail Settings page. If the user had already logged in to GMail before this change was done then he may need to logoff and login back to get the changes reflected on the settings page.