Order Categories and all custom taxonomies terms (hierarchically) using a Drag and Drop Sortable javascript capability. No Theme update is required the code will change the query on the fly.
If multiple taxonomies are created for a custom post type, a menu will allow to chose the one need to be sorted. If child categories (terms) are defined, those can be ordered too using the same interface.

Also you can have the admin terms interface sorted per your new sort.