Now you mention it, I am not a big fan of the "flat list" organizing principle, as popularized by iTunes. If you can think of anything to better organize bookmarks, you might be on to something. However, I also usually prefer to keep them on my local computer and not to share them with the world.

"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.

I use my bookmarks as a "read later" list. So I remove them once I have read them.

By the way Google does let you also tag (label) the bookmark. It's just that you have to press a different button to do that. Supporting both methods like Google does would work pretty well.

I thought I was the only one who uses the bookmarks for things to "read later".

Yes, Google let's you label the bookmarks. However, I was curious about the preference for a flat list that some people seem to like. Would a bookmarking site that doesn't have tags nor folders be something that people would like to use?