I have a question on how we "should" structure the directories for our  
software (for loose values of "should").

Is there a guideline that prefers one of the following over the other,  
given the company ACME and the program WidetApp, or is it just  
tradition etc.?

1) C:\Program Files\ACME\WidgetApp
2) C:\Program Files\WidgetApp
3) C:\Program Files\ACME WidgetApp

I see in the WiX 3.0 documentation #2, i.e.

<Directory Id="TARGETDIR" Name="SourceDir">
   <Directory Id="ProgramFilesFolder">
     <Directory Id="APPLICATIONROOTDIRECTORY" Name="My Application  
Name" ...


Gabor Deak Jahn's wonderful WiX tutorial has, #1 for example:

<Directory Id="TARGETDIR" Name="SourceDir">
   <Directory Id="ProgramFilesFolder" Name="PFiles">
     <Directory Id="Acme" Name="Acme">
       <Directory Id="INSTALLDIR" Name="Foobar 1.0">

If I'm interpreting the output of heat, I see #1.

<Fragment>
   <DirectoryRef Id="TARGETDIR">
     <Directory Id="dirGUID1" Name="Acme" />
...
<Fragment>
   <DirectoryRef Id="dirGUID1">
     <Directory Id="dirGUID2" Name="WidgetApp" />

If I look at my Windows Vista Start button, I see many instances of #3  
in the form Microsoft Foo or Windows Bar.

Microsoft Office PowerPoint Viewer 2007
...
Windows Calendar
Windows Contacts
...


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