You know how some guys paint shadows on the pegboard to show where a tool goes? I do that as well, but improved it to match my style by just painting a big splotch on the bench to show where the pile goes.
Seriously, that's an awesome setup. My work space is dedicated to my pottery studio, so all my bike parts are stored in a much smaller space. I use plastic storage tubs with lids to keep like parts together and find-able, one for suntour, one for shimano, one for misc deraileurs, brakes, one for posts, two for stems, several for cranks and rings, and so forth.
Additionally, those zippered plastic bags that sheets or pillow cases come in are handy for storing individual parts in to keep them from getting scuffed. I store all my freewheels in these, as well as brake levers and things. Keeps crank arms together. Little parts are in two of those hobbyist pull out drawer organizers.
All my tools pretty much fit into one of those bucket buddy things, but I am looking for a better mobile solution. It gets over full.
And my work stand was built by a backwoods redneck savant out of various pipes and the like back in the seventy's. Its very mad max, but works well enough. I'd be embarrassed to show it though. Until recently student loans took priority over a new stand. Soon as I take care of all the other things that I put off to pay Sally Mae, I might upgrade.