Bookmarks. They accumulate like lint on Uncle Mikey's chin on Sundays after his tenth beer and third football game. I truly feel your pain. Fortunately, a little scrounging and a few nice hot cups of tea shared by the extended TUAW family may have unearthed a few solutions for you.
You don't mention in your e-mail which browser you are using, so let Auntie point you to solutions for both Safari and Firefox.
On the Safari side, Uncle Chris White tracked down Balooba software's Safari Prariefire, which scans for dead, missing, and duplicate links. It's shareware and costs US$6. Currently all registration fees are being donated to the Red Cross in support of the Japanese earthquake victims.
There's also a trial version for getting a feel for the software prior to purchase as well as a "free" version if you're willing to go through TrialPay, a service that frankly makes Auntie uncomfortable -- it's a creepy "sign up for stuff" option that doesn't seem entirely above board.
On the Firefox side, there's CheckPlaces. CheckPlaces is donationware which adds the same kind of checks for valid pages and duplicates as Prariefire plus empty-folder and favicon completion options. CheckPlaces will also "compact and check the integrity" of your Places database.
Between these two, you should be covered -- unless you're using one of those newfangled longhair browsers like Chrome, Opera, or Lynx.
Auntie sends her love. Don't forget to brush and floss -- good dental hygiene is a gift!