Here's UT's Clay Spinuzzi demonstrating a highly sophisticated annotation system the night before ATTW 2005. Note the use of two meaningfully different colors of Post-It Notes. (Well, meaningful to him at least.) This shouldn't come as a surprise; Clay's very aware of his own literate processes (see also: his "Encomium on Sticky Notes").
Clay Spinuzzi coordinates text, oh yeah!
A coordinating madman.