I have a folder with various document files on my various theories and work. I used to go with the earliest ideas at the top and then work downward. Now I've reversed that and have the newest ideas at the top, so I start out looking at the latest things. I bold the main concept that made me want to write that thing down, so I can skim the file easily, and then under that use hyphens with each thought or longer statement relating to it. So a typical entry looks something like this. (for some reason I can't do hard returns so...it actually wouldn't look like this at all.)

Ted Williams called his book "The Science of Hitting." -This type of phrase might be good if we want to collect this as a book. -We can go to wikipedia later and see how the book was received.

If I have a breakthrough, I put it in red, and if I quote something or have something interesting, it's in italics.