We learned our lesson the hard way.
In Windows 95, we gave programmatic access to the Start menu "Fast items" list - the items that appear at the top of the Start menu above the Programs list. This area was meant for the user to customize with their favorite links, but programs quickly saw the opportunity and spammed themselves into it every chance they got.
In IE, we gave programmatic access to the Favorites menu, and once again, programs spammed themselves into it.
In Windows XP we intentionally did not give programmatic access to the bold list of items at the top of the Start menu (the "pin list"). The pin list is for users to put their favorite icons. It is not the place for a program to decide unilaterally, "I am so cool. I am your favorite icon. I just know it. So I'll put myself there because, well, I'm so cool."
Because we knew that the moment we let people mess with the pin list, everybody would install themselves into it and it would become meaningless (and annoying).
What's particularly galling are the programs that, as part of their install, decide that they are so cool they want to be everywhere to make sure you don't miss out on the coolest most amazing program ever written in the history of mankind, so they go into the Start menu, into the Fast items, onto the desktop, into the Quick Launch, onto your Favorites, take over as your default autoplay handler, and even hang out as an icon next to the clock on the taskbar just in case you somehow missed all those other places - and each time you run them, they go and recreate those icons and settings in case you "accidentally lost them".
I hate those programs.