Taking notes is the obvious one.
The pen combined with an app like Samsung's Scrapbook is great for organizing things you want to remember. Places to go in the future, gifts to buy for the wife, things to get for home projects, etc.
Annotating screenshots has been useful for me. Sending friends a quick pic with added instructions written by me, or circling something hilarious and sending a screenshot.
Web browsing works well with the pen. The fine point allows you to browse desktop style sites without needing to zoom in just to tap things.
It also works for certain games, for example the enhanced editions of Baldur's Gate or Icewind Dale. Without the pen I would never try playing those games on my phone.
The pen is the one reason why I'm still considering a Note 5 along with the new Nexus 6.