Hi
Most programs are installed into the "All user group" this is why they show for both users,
Go into Windows Explorer and go into the Documents and setting \user\start menu for each user, as you will find they both have identical program groups\accessory groups. You can edit these as you wish so that the users only see the programs you want, however any PC savvy users will know they can access the program by going into explorer and finding the shortcut for it in the program group.
As for IE6 favourites, they should be different for each user that logs on as each will have their own profile and its here where they are stored. I dont know why they are identical.
Regards