If you are using AD Domain accounts for your users, and the QlikView Server service is set to security = NTFS (check your QMC for the actual setting), then it may be a simple matter of adding group Domain Users to local group Users to give all users READ access to the QVW documents...
1. Do the users have the read access to the folder(s) with the missing apps?
2. Is the Folder set to browsable in the QMC? (System -> Setup, select the QV server and check the Folders-tab and the "Browsable" check-box (don't forget to apply if you change it)
3. Have someone deselected the Availability on the document(s)? Check in the QMC, Documents, Select the document and look in the Server-tab, in the Availability-subtab. Check that the "Access method" has check marks in the client type you are using (IE client and/or Ajax). If you need to change you must hit Apply for each document.
4. If you are using Section Access - does the user have USER-access to the data in the document? If not QlikView will hide it from the user.