You can have virtually instant access to ALL your Safari Bookmarks from the Bookmarks bar (via heirarchical menus) if you spend a few minutes sorting them. Create 6 or 7 (max) main folders (e.g. Personal, Work, Family, Education, ...) and put those in the Bookmarks Bar. Then sort your bookmarks into sub-folders, and put all sub-folders into the appropriate main folders.
Also, for grabbing bookmarks quickly while surfing and putting them where they can be easily found/sorted later, use an INBOX in the Bookmarks bar. Create a new folder in the Bookmarks window, call it INBOX, and make it the first item in the Bookmarks bar. Then while surfing, you can just grab the icon to the left of the URL, and drag it to the INBOX on the Bookmarks bar.
After following these steps, the only time you ever need to open your Bookmarks window is when you want to sort any new bookmarks you have collected.
[robg adds: This bookmark organization hint will apply to any browser that supports folders on the bookmarks bar along with sub-folders, which I think is pretty much all of them now ... and yes, it's a simple concept that many of us take for granted, but it's probably of use to some of the audiience at large.]
Mac OS X Hints
http://hints.macworld.com/article.php?story=20040304200401969