Though I don't have any need for this package atm, I see that it might be useful in certain special cases. Since in addition to listing installed apps it also allows to store configuration it offers more functionality than checking which packages were installed using the PEAR-installer.
Maybe an (optional?) indicator for the version of the configuration-data would be nice? This way there would be a central place where a program can look if the config comes from an old version and automagically convert it. However, this could surely also be implemented by the app-developer directly in the stored configuration-data. But he would need to check for every layer again and there is no central storage for an (optional) version-number.
Also, might it be a good idea to be able to list the configuration of other users than the current? Maybe using "user::<username>" or similar? And what if you have several "users" running as one actual system-user? Maybe there could exist sub-users so that a web-app could store settings for a number of users of the same application?
The hooks also seem useful.