Galaxy Note 3 - Is there a way to add more apps to use when drawing a 'Pen Window'?
Without root it is up to the developer of the particular application, and chances are there aren't enough Note 3s out there to justify it.
There is an S-Pen SDK from Samsung
There are lists (but these will often be out of date in no time)  like this best S-Pen apps out there.

With root access  there is a way to open any app in Pen Window Mode

First, make sure you are rooted with busybox installed.
Second, make a backup.
Third, just download PenWindowManager_v1.apk  and install as normal.
Finally, just tick the apps you want and don't forget to press the save button. A soft reboot maybe required for the changes to take effect.