"I also usually prefer to keep them on my local computer and not to share them with the world". You could keep it online, without sharing it with the world. This should be done with a transparent encryption scheme. The server stores only the encrypted version of your list. Your browser decrypts it and shows it to you, wherever you are. This should work for anything where searching/indexing is not needed. Sadly, this would remove the possibility of targeted advertising, which is the main (only?) source of profit these days.

database tables are a flat list, but that doesn't mean that the they aren't organized. I usually search my flat list of bookmarks chronologically and by searching for some keywords.

I guess you could map the whole universe to a flat list, that wasn't my point ;-)

With iTunes or thousands of bookmarks, I find that I can't "stumble upon" things anymore - I have to know what I am looking for, so that I can search it. I used to have my music simply organized in folders, and it was so much easier to browse (and still searchable).

Of course the iTunes style allows for new ways of stumbling across music, like "all songs that beginn with the Letter A", but I prefer the "old way" so far.