I'm pretty sure it would not be very difficult to implement color coded stickies.
A DM could use blue stickies for secrets the player's need to roll perception for. Green stickies for Initial setup instructions. Red stickies for story or RP suggestions, etc. These are obviously just suggestions, but I'm sure over time the community would develop a soft 'standard' that makes it easy for everyone to browse through level instructions.
Folders are great for managing/organizing stickies at a macro level, but for stickies in the 3D world a little color would go a long way.
