Bookmark Sorter can automatically keep your bookmarks sorted according to your preferences. The app is able to alphabetically sort your Safari® bookmarks, place your bookmark folders at the top of the bookmark list, rename bookmarks that have the same name, and remove duplicate bookmarks.
Since Bookmark Sorter is a regular application you can manage it as you do any of your applications. If for example your preferred way of starting an application is through the dock, then Bookmark Sorter will happily live in the dock for you.