Why are bookmarks in the web browser only? It seems so limiting to me. Shouldn't any file or folder be bookmarkable?
Anyway here's my idea. Remove the bookmarks menu from every application that has one. Instead add a "Bookmarks" menu to the desktop panel menus. This menu would list the 15 most used  bookmarks and a "More Bookmarks..." menu item. Selecting "More Bookmarks..." opens the bookmarks folder , giving you access to all of your bookmarks and automagically opens them in the correct application.
How do I bookmark a page than? Well quite simply File->Bookmark should be available for every document. 
Question and Answers
Well hierarichal menus are slow and hard to use. The main goal of the bookmarks menu is to provide quick access to the most commonly used bookmarks. Including all bookmarks in the bookmarks menu makes the menu inefficient at which point a desktop launcher to open the bookmarks folder makes more sense. The bookmarks folder should provide quick enough access for less commonly used bookmarks.
File is the most correct menu in which to place this entry. All document actions appear in this menu including print and save.
 Note I say "most used" and not "most recently used" there is a difference.
 I use the term "folder" loosely here, it need not be a unix directory.
 Of course for this to work we're going to need a cross-desktop standard for bookmarks.
 This assumes a hierarichal bookmarks system of course, which I actually don't support but thats another issue.