There is an easy way to force a few of your menu items to the top of the alphabetical list without renaming them.
For example, if you change "Scrapbook" to " Scrapbook" (with a leading space), then it appears in the Apple menu ahead of "AppleCD Audio Player" and "Chooser".
In the Finder, open your System Folder, then your Apple Menu Items folder, and change the names of the menu items as you would any other filenames.
You might also want to experiment by putting various punctuation symbols at the beginning of the items in your Apple menu to see how this affects the sequence. If the menu is cluttered, make an empty folder named simply with a row of hyphens, or any other character, and use it as a divider with leading spaces to position it appropriately between, folder aliases and application aliases in your menu.