A system instituted in the latter
Middle Ages to differentiate relative importance of
headings or sections of a book. Roughly speaking, the more important a heading is, the larger the letters are, the older the script used to write it, and the more expensive the pigment used to write it in. Hence, a really involved book might have, in decending order of importance:
Roman Square Capitals (gold)
Uncial Majuscules (purple)
Uncial Minuscules (green)
Gothic (blue)
Italic (red)
Humanist hand (like print, but handwritten) (black)
As you can see, this allows for all kinds of fun tricks with capital letters vs. caps-plus-smalls, relative colors, etc. You can use the color hierarchy to distinguish between different ranks within hands, or vice versa, or even use different sizes within each hand/color, as long as the basic system is kept. Normally, of course, most books would be written in black only, or black-and-red, and the other colors added as needed if it got more complex. You can see how this might have come about as successive generations added commentary on older texts, or as older bits of manuscript were bound with new ones. I once did a set of lecture notes in this manner for an art appreciation class with ClarisWorks 4, printed with a simple inkjet, and people were fighting to get my printed-and-cleaned-up notes at the beginning of each class. It's a fun concept to perk up your linear algebra, logic, or other post-calculus math notes too! (John Nash once swore by the use of colors in math, but you know how he could be...)
If this all seems just too, too, academic, think of how you were taught to write outlines in grade school...