The new, two-rolled-into-one /Apps folder is the equivalent of the old /Apps folder in that everything in it is available to all users, but the Apple apps are protected, while the 3rd party apps are writeable, i.e. can be trashed.
User by user apps are, as always, stored in ~. If you create a new folder in that location and name it "Applications," it takes on the /Apps icon rather than a generic one.