This app was mentioned in 6 comments, with an average of 5.50 upvotes
https://play.google.com/store/apps/details?id=com.tushar.cmspen2
&
https://play.google.com/store/apps/details?id=com.tushar.spen_helper&hl=en
I run these two programs on CM12.1 and they work pretty well. Albeit I don't use the S-Pen much.
CM13 on a Note 10.1 here. The S Pen itself works perfectly. System-wide palm rejection works, pressure sensitivity works, the pen button works (Tested using Google Photos. Holding the pen button and swiping up or down controls the zoom.), but almost no apps use it. The tablet can even still detect me hovering the pen (Tested using Autodesk Sketchbook), but again, almost no apps actually respond to the user hovering the mouse pointer. There's even an option in Language and Input to show a mouse pointer icon when you hover the pen.
However, TouchWiz specific features aren't available. That means no Air Command, no turning on the screen when you take out the pen, no S Note (you'll have to use a third party note taking app), no taking screenshots by drawing a box, no scrolling by hovering the pen over the bottom of a menu. Some of these features can be mimicked by this app, but for it to work you'll either have to set SELinux to Permissive or install SuperSu. You also have to pay to unlock a lot of the app's functionality.
TL:DR
Download the apk from xda: http://forum.xda-developers.com/galaxy-note-3/themes-apps/app-screen-off-memo-t3196790
Set as device admin.
This also works on notes without touchwiz, with a helper app: https://play.google.com/store/apps/details?id=com.tushar.cmspen2
Edit- The apk is from a developer called xperiacle, looks like his thread is here: http://forum.xda-developers.com/galaxy-note-3/themes-apps/app-screen-off-memo-t3196790
Just saves you having to go to a YouTube video, then to someone's blog, just to get to xda.
I recently installed Temasek CM12.1 v10.7
http://forum.xda-developers.com/galaxy-note-3/development/hlte-spr-vzw-temaseks-unofficial-t2953375
It's Android 5.1.1, the absolute latest. Overall it's the best Android experience I've had. The phone is way faster without Touchwiz.
There is an App for the S-Pen. I don't use it, so no idea if it works:
https://play.google.com/store/apps/details?id=com.tushar.cmspen2
Also, the stock playstore Hulu doesn't work. You have to revert back to version 2.12. See this thread:
https://www.reddit.com/r/GalaxyNote3/comments/34bl1d/hulu_not_working_on_temasek_cm121_v107/cqt8io6
Lastly, have a look at reviews here:
https://play.google.com/store/apps/details?id=com.tushar.cmspen2 can detect that (paid)
There are a couple apps you can install to help you on an AOSP rom.
CM S-Pen Addon (Root) https://play.google.com/store/apps/details?id=com.tushar.cmspen2
Note Buddy (S Pen Helper)
https://play.google.com/store/apps/details?id=com.tushar.spen_helper