For your requirement you can try the following,
1. Create a Region entity in you App module with attribute Name and set many-many association with the Timezone entity in System module (Reference Set - Both).
2. Create a Region setup page with Datagrid and new/edit page.
3. In New/Edit page add a reference set selector for the newly created association. So your objects will be like Name : 'Pacific' Association : Set of TZ's that come under 'Pacific'.
4. To test this go to Accounts Overview and add a New Column for Region select the Region.Name through Account-User-TZ-Region association. Same can be done in the reference selector in Account New/Edit page for the Time Zone.
Hope this helps, sorry would have been easier with Screen Shots but I am not allowed to do so. :P Good Luck!