You can disable some Autoresponders at: Admin panel -> Settings -> Tickets on the Auto responder tab.
IT says on that page "disabled at department or email level."
If you go to Admin panel -> Agents -> Departments and click on a specific department, you can disable Autoresponders for that department (so if your Users tickets go to a specific department you can suppress them).
If you go to Admin panel -> Emails -> emails and click on a specific email there is a check box for Auto Repsonse. So you can over ride it there.
Organizations do not have an override for these settings however.
You could also set a fake email address for the users that do not want emails. (fake@faux.net) I imagine that might result in some other issues though (like bouncebacks).
