We then got a bookmark system that was every bit as terrible as a web directory.
It stayed that way. The delicious search revenue made organizing websites uninteresting. That obscure website you enjoyed a decade ago but don't even remember, they had lots of traffic like you. No point updating or keeping it online. You can't have rss in Firefox but here is a Facebook like button in your address bar in stead.
I've tried to maintain the bookmark menu but I rarely use it since everything is dead. Why aren't browsers storing a text version of the bookmark? Did people in 1993 have more resources than us? Should I be afraid it grows to a few GB over the decades?
A good few dead websites have a backup some place but there is no automation to find it. If you had a string of text from a page you might be able to search for it. If the page found is highly similar we might automate the process to have alternative location for bookmarks with a nice warning dialog.