Using Date Popup widget with custom format Date field
Drupal's Date module includes a 'Date Popup' sub-module which handles date pop-up widgets. These widgets are available in the FAPI (form api) and can be configured with custom formats via the #date_format property. 

You could implement hook_form_alter() and change the #date_format property on the date field you're working with. I believe this property will support all formatting available in PHP's standard date() function.