I run Ubuntu from Live CD and want to retain settings and downloaded apps from the session. Does Ubuntu allow a configuration file similar to Puppy Linux that can be saved to the system's hard drive?
I have found this on the Ubuntu wiki : https://help.ubuntu.com/community/LiveCD/Persistence.
I believe that it will allow you to do what you want.
Here is one for USB sticks: https://wiki.ubuntu.com/LiveUsbPendrivePersistent