How can I put a permanent custom format for time in excel??

As mentioned, the Custom Number Formats are retained within the workbooks but if you add your custom format to a blank workbook and save it as either your default BOOK.XLTX template or a custom Excel template within the User Defined or Workgroup templates, it will be available for all new workbooks opened via that template.

If you have some other tasks (e.g. Page Setup, Zoom, etc) that you repeatedly make, you can make those changes at the same time. Some changes are global to the workbook and others are to each worksheet within the workbook. You can make changes to all three blank worksheets as detailed below.

Please review these Microsoft Support articles for further information:

How to manage templates in 2007 Office programs
http://support.microsoft.com/default.aspx/kb/924460?p=1

Customizing Excel defaults with templates
http://office.microsoft.com/en-us/excel/HA010548151033.aspx
(note: This applies to Office 2000 and needs traslating to 2007. The 2007 default template location is C:\Program Files\Microsoft Office\Office 12\XLStart\)

I wrote this followup for changing Page Setup for 2003:

Page Set Up Default
http://social.answers.microsoft.com/Forums/en-US/excslcreate/thread/41410294-3abc-4450-936b-0c21db7cddaf