Do we really need/want the winefile link on the desktop? Especially since it is also present in the start menu now. If I recall correctly, the Command Prompt was put on the desktop 'cause at the time it was the only viable way to start programs, I think maybe even the Command Prompt link could go from the desktop now.
If you want, you can comment out the two desktop shell links. The start menu may be seen as enough. But I think the desktop is big enough to hold some convenient shortcuts. Just another thing, where there is no "correct way" per definition. Personally I never understood why MS removed all icons but the recycle bin from the default desktop in XP.
Regards,
Martin