If you paid really close attention to the way a representative shortcut is selected for a program, you may have noticed a problem with it. Here's the rule again:
If there are multiple shortcuts to the same program, then the most-frequently-used shortcut is selected as the one to appear on the front page of the Start menu.
Suppose there are two shortcuts to Notepad on the All Programs section of the Start menu, one is the standard Notepad shortcut that comes with Windows, and the other is a shortcut whose command line is
notepad.exe C:\Program Files\LitWare Inc\Release Notes.txt. Now suppose the user opens a text document on the desktop. Notepad runs, it "earns a point", and suppose that this gives Notepad enough points to appear on the front page of the Start menu. Which Notepad shortcut do we show?
According to the rule stated above, we will choose either the standard Notepad shortcut or the LitWare Release Notes shortcut, depending on which one you've run most frequently. If it's the latter, then you'll have the puzzling result that opening a text document on the desktop causes the LitWare Release Notes shortcut to show up on the front page of the Start menu. It's perfectly logical and completely baffling at the same time.
In Windows Vista, another tweak was added to the algorithm by which a shortcut is chosen to represent a program on the front page of the Start menu: If the user hasn't run any of a program's shortcuts from the Start menu, a shortcut that doesn't have any command line parameters is preferred over one that does.
This tweak causes the Start menu to favor the standard Notepad shortcut over the LitWare Release Notes shortcut. It also means that, for example, a shortcut to
Litware.exe is preferred over a shortcut of the form
Note: I was not present at the Windows Vista Start menu design meetings, so I have no insight into the rationale behind its design. Sorry.