Not all genealogists understand how this works, so you find many sites that have a title of index.html or new page or something equally vague. When saving the URL to a given folder, it is important to verify that the name being saved is understandable. A folder full of sites named index.html is no better than massive bookmarks in no particular order. The title of the site, regardless of what the webmaster named it, should mean something to the researcher. If it doesn't then the researcher will continue to have difficulty locating that URL regardless of how the bookmarks are organized.
Most researchers categorize their research under surnames and localities.
These are perfect for creating folders. For professional researchers these folders can take one additional step. The initial folder could be the name of the client and sub-folders can display the names of the surnames and localities researched on behalf of that client. When creating folders for bookmarks, it is important to think about the scope of the site's information. Folders traditionally go from the largest to the smallest in scope.