i'd love to see a simple note taking application that was focused on facilitating that workflow.
You might want to look at The Literary Machine http://sommestad.com/lm.htm
From the website:
What The Literary Machine can do for you
Creativity is not "connecting the dots" with a graphic program that weaves a web among them all over your computer screen. Creativity is seeing which dots are connected. In groundbreaking, ingenious ways, LM helps you do that. What makes LM different from other idea-generators? It doesn't pass off rote as thinking. Instead of showing you a generic list of logical formulas to wade through in hopes that one accidentally manipulates your ideas in some meaningful way, it works with your mind, illuminating connections and stimulating insight.
The Literary Machine is a dynamic archive and an idea management tool aimed at creative thinking — built especially with the writer in mind. It is packed with indexing and display techniques so general and potent that you will use it as an intelligence center. In a class by itself, it is virtually an extension of your brain. So, write in it. Collect and sort information and ideas in it. Make it your treasure chest of random notes and ideas for analysis and future reference. For, it will serve you well as the substance, catalyst, and processor for relating or reusing them in creative combinations.
LM is designed to fulfill needs, not fancy. So it does not fool around with features that your conventional word processor and email client already do well and more efficiently than a database could. Instead, LM teams with your other programs to accomplish what, till now, was possible only in your dreams.
Minor hyperbole aside, it does pretty much do what it says. If
you can work with it.
The major problem with "thought processors" is that each has a process style and philosophy (or a "strategy" if you're an NLP fan). If that doesn't match your way of thinking or working, and you can't adapt or learn the app's methodology, then you're out of luck no matter how good it is. I've run into that with IdeaFisher. People whose opinions I respect have raved about it. I found its methodology unworkable. I do like Dramatica Pro. I use it to vet my story structures. I think it's great and easy to use. Almost everybody else I've talked to thinks it falls somewhere between cumbersome and flat-out useless.
There is also the problem of the learning curve. The Lit Machine is very up front about this, perhaps because that's the chief criticism leveled against it.
A word about the learning curve:
LM's core database features are highly intuitive and easy to learn. But learning to use all the program's capabilities is another matter. LM has such extraordinary capabilities because it is an unusual program. Consequently, it takes time to learn.
Such power always comes at a price. To make a powerful program do what you want, you often must learn techniques and procedures, not just where to find this or that command. (If you are familiar with high-end graphics software like Adobe™ Photoshop, you immediately see what we mean.) Don't worry: LM's learning curve is nowhere near as steep as that of high-end graphics software. But it is steeper than that of most freeware and shareware. So, be forewarned: you probably cannot master LM's Project window in a day.
Therefore, we do not recommend this program as a solution for an important project that now has you up against a deadline. Especially if you're not technically savvy and have never worked with a sophisticated database before. And we do not recommend LM for people unwilling to read the documentation, view the slide-show animations, and study the tutorials. Also, we suggest that you establish a second instance of the program on your machine to serve as a practice database. You'll learn faster, because you'll experiment more — knowing that your main installation and its important data are safe from a beginner's mistakes.
If you plan to buy the Professional version, it is a good idea to try LM2000 first. We can help LM Pro users with individual mail support, but we cannot guarantee that everybody really likes the basic ideas in the LM program design.
So there you have it. A very interesting application with a version free for the download.