I guess if you really want the full s-pen experience you need to be running a Touchwiz based rom. The ability to force apps into a tablet interface is a much bigger deal in my day to day use. With such a large screen it makes a big difference for apps that support alternate UI.
As for apps. There isn't much in the way of killer apps that specifically take advantage of the s-pen. Mostly drawing apps. I use the autodesk sketch one on my note. After the initial "wow I have a pen!" of the first couple months I mostly pull it out for drawing on games like drawsomething, art programs, and occasionally while web browsing to select stuff easier without zoom.