Items in your Apple Menu are located in a folder named "Apple Menu Items" within your System Folder. Anything that is placed in this folder will show up in your Apple Menu. Items in your Apple menu are arranged in alphabetical order. Knowing this allows you to arrange the items in your Apple menu. Some thing that makes this easier is the fact that non-alpha-numeric characters fall above and below the alphabet. (Without going too far indepth, the order starts with "space" and goes through most of the non-alpha-numeric characters then the numerals, alphabet and ends with "odd" characters [*,+,-,.,=, 0-9,a-Z, {insert charaters that fall outside normal}]) I'll try to find a definitive list and post it.
A good tool for organizing your Apple Menu Items is Amico
Another thing to remember is, whenever possible, use aliases in the Apple Menu. Some applications, such as FrameMaker or any Microsoft product, need to be kept in the same folder as their support files in order to fully function. By making an alias of the items that you want to put into your Apple Menu, you also leave your actual File Organization intact.
With the exception of the Chooser, all of these items are Folders. Most of them are aliases of folders on my Hard Drive. This may seem odd, but I am using System 7.5 and my Apple Menu is Hierarchial so this method gives me complete access to my files without cluttering up my Apple Menu with Items that I only rarely use.