To put it straight, ProgramData contains application data that is not user specific.This data will be available to all users on the computer. Any global data should be put in here.
AppData folder contains configuration settings, downloaded information/files for a particular user. So, for example any user specific preferences and profile configurations can be stored in the AppData folder. The AppData folder is further divided into three subfolders
Roaming – This folder contains data that can move with your user profile from a computer to another.
Local – This folder contains data that will not move with your user profile.
LocalLow – You can put in lowlevel access information such as information related to web browser running in a protected mode in this folder.
You can now decide depending on the type of information which would be the best place to store it.
Reference links: Windows CSIDL and AppData