Here is a neat tool to tidy them up.
Tidy Favorites allows you to organize your bookmarks visually. Bookmarks are sent to a separate browser tab and the bookmarks with thumbnail images.
This allows you to easily see and manage all of your bookmarks with just a glance.
If your bookmarks have gotten out of control try this free software.
They have both a Windows and OS X versions.
http://www.tidyfavorites.com/introduction.html
