Proposals
The people who want to succeed at note taking are going to succeed regardless of the tool or method. This initiative is for those of you that would prefer to put in less effort.
Write First, Think Later
What matters initially is just the context of the thought. If you're browsing your notes and a note sparks a thought, creating a note on the spot should link the two (of course, you don't need to). If you have an idle thought about your novel, all that matters initially is that you were thinking about your novel. You can connect the details later.
Build for Browsing
When writing notes, link to other notes whenever possible. Referencing and reviewing other notes reinforces your mental map of your knowledge base. When viewing a note, also show notes that link to this note.
Don't Lose Track
As you browse notes, your note history is visible, allowing you to flip between notes seamlessly. At any time, you can check out notes and place them for review. This allows you to view multiple disparate notes at the same time. If the review was fruitful, you can automatically link all of those notes together.
This Looks Important
At any time, you can pin a note and pool it to the top of the space that you're working in. It's hard to know upfront where the important waypoints for a series of thoughts are going to be. Also, surface the most linked notes.
Keep it Focused
Try to make each note about one thing. Because it's so easy to lose the point and lose interest as a note drags on, notes will have a character limit (think like, 1400 characters maybe). Once a note exceeds that character limit, another note is created and automatically linked to the previous one.
Check The Bin Occasionally
Notes that are old, never linked to anything, or recently deleted should occasionally surface in a designated dusty corner in your peripheral vision. Maybe it'll spark an idea? Or maybe it'll help you let go of another.