[Galaxy Note II Q&A, Help & Troubleshooting] Acorns:
The Samsung Keyboard:

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If you select the Samsung Keyboard in Settings->Language and Input you can use the S-Pen for handwriting recognition input anywhere you can use the keyboard. To activate handwriting recognition, press and hold the microphone icon on the keyboard:

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Then select the 'T' text input icon:

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Write in the center box that appears. The system will turn your input into text with a slight delay. It is quite accurate and can even interpret cursive - if your cursive is very clean and proper.

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While in the keyboard, draw a line from left to right to put in a space. Draw a line from right to left to press backspace (you can also just tap the backspace icon on the top).

Tap the 'A' icon at the top to change the keyboard to numeric input mode, which is more accurate at recognizing numbers and equations.

Tap the '123 Sym' icon to bring up a quick, tappable menu of numbers and symbols.

Press and hold the microphone icon, then select the keyboard icon to return to the normal keyboard.

Quick Command:

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Quick command can be used anywhere on the device to take a predefined action or execute a macro. Access quick command by pressing the S-Pen button and drawing a line from the bottom to the top of the device. Any length of vertical line should work, it doesn't need to be precise.

Once the Quick Command screen pops up, you can draw one of the predefined icons followed by text, or define your own macros. To define your own macro, press the settings button in the upper right of the Quick Command screen, then add a command. You can open an application or select functions. In functions, you can set more than one action. "Mute and enable bluetooth" for example. Once selected, you can draw or select one or more characters and symbols to activate the action, and then use those symbols in Quick Command!

S-Note:

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S-Note is one of the applications always pinned to the bottom icons in the Touchwiz Launcher. It is the showcase app for the S-Pen.

If you take partial screenshots with the S-Pen and send them to S-Note, they will appear in the Scrapbook.

To create a new Note, use the '+' icon. You don't have to be in a folder.

Once in a note you can write and draw as you wish. Hover over icons to see their functionality, or press and hold them to bring up more options. The third icon on the top row allows you to switch between drawing, formula match and text input modes.

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While in drawing mode and not touching the screen press and release the S-Pen button to switch between eraser and draw modes.

Tap the image icon for a menu allowing you to insert pictures, video, etc. This menu can be scrolled down for more options, if in landscape mode. One cool option is 'Idea Sketch'. After selecting it you can write the name of something you want a quick image of, and the device will search for it.

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Tap the red circle icon to begin (and then stop) recording your drawings as a video. To playback these recordings close and save your note, open it and press the 'Play' button.

A full, useful tutorial on S-Note can be found by pressing the menu key, scrolling down in the menu and pressing Tutorial.

I'm sure I've only scratched the surface of what is available when using the S-Pen. If you have any new tips or tricks, or want to write up a section on another app that uses the S-Pen, make a post and I'll add it to the reference! I also plan on making an S-Pen quick reference screen in the future, if there is any interest.