Firefox only: If your bookmarks bar has gotten out of control with dead links, duplicates and empty folders, Firefox extension CheckPlaces will check all your bookmarks and even clean them up for you, automatically deleting anything unnecessary.
The extension is extremely configurable, so you can choose what you want it to check for — if you have duplicate bookmarks on purpose, for example, you can have it just check for dead links and empty folders. You can also choose to individually exclude specific bookmarks from the check, if, for example, you think you may have unwanted duplicates but want it to ignore duplicates you made on purpose. It can even load favicons for websites you may have imported, but haven't visited yet.
After you select your options and run the check, a window will appear summarising any issues you may have. From this window, you can look in each category (failed pages, duplicates, empty folders, etc) and pick which bookmarks you want to delete, or just delete all bookmarks in that category. You can also choose to exclude certain bookmarks on this list from future checks, so you don't have to worry about singling them out anymore.
CheckPlaces is a free download and works in Firefox on any platform.
CheckPlaces [Mozilla Add-Ons]