Windows is an operating system that is designed with a single user in mind, with some multi-user features added on later. Usually in a quick and dirty sort of way to make some large client happy.
So, you don't have very fine grained control over these sorts of things. A lot of settings are shared among all users, and that includes some programs like QuickTime, that will load before any user even logs in. You could disable it using msconfig and then add it to individual user's startup folders, but this would quickly become a nuisance if you need to do it with more than 2-3 programs for more than 2-3 users.
The ultimate result is that there is no good way to manage these sorts of things. It's a result of the very design of Windows, so until that changes, you're stuck. If I were you, I wouldn't waste my time trying to fight these things. You might want to limit the number of them, but don't waste your time fighting a losing battle.
I've been working on setting up individual users for my family on my computer and I was wondering if it was possible to create indidvidual startup preferences for each account. i.e. to be able to have quicktime load as a startup item on one account and not on another. Don't know if you can through msconfig or not. Thanks in advance for any help.