You can have folders with .qvw:s inside them.
And then set NTFS AD group permissions on the folders, and use inheritage.
So each .qvw inside the folder inherits what is set on the folder.
You can then have folders which are open, all users can see the docs.
And folders with ad group permissions.
And .qvw:s which only specific users can see.
Most of the replys are pointing you in the correct direction. If you don't have publisher you will have to set NTFS permissions on the files. You can also do this through DMS security. If you set the server to DMS mode you will find an additional Tab "Authorization" where you can add the users.