To that end Apple has pretty much left the bookmark structure in Safari untouched. Maybe there’s no better way to handle hundreds of bookmarks, but there are different ways, though some of the best have shortcomings.
I’ve been using Momiji on Mac, iPhone, and iPad. It’s a bookmarking app that runs on all three devices. First, Momiji can import bookmarks from your favorite browser. Bookmarks can be synced with Pinboard, synced over your local network or Wi-Fi. Oddly, there’s no iCloud or Dropbox sync, which would seem to be a plus.
Momiji is a standalone app and Mac users can incorporate bookmarks into Safari, of course, but also Google’s Chrome, and Opera, but– here we got odd again– not Mozilla’s Firefox.
Skeumorphism aside, Momiji is an attractive bookmark manager for Mac users who are serious about bookmark management. You can add notes to a bookmark, add tags for faster searching, and even share bookmarks to Facebook and Twitter (and OS X’s Mail app, of course).
Searching through hundreds or a few thousand bookmarks is easy, but only after you’ve organized bookmarks, added tags, and cleaned out the cruft. That’s a laborious task, perfect for the OCD afflicted.
Momiji encrypts bookmarks for added security but without iCloud or Dropbox sync, it’s an effort piled upon effort.