i have a 2 drawer rally box that does all the bread and butter work. its loaded and disorganized but fits everything i need for the most common jobs. also have a mechanic style tool box under the bench.
The goal is to have them immediately accessible and within easy reach. I have pegboard and a roll-away toolbox in my basement shop, but I have a my most commonly used tools and supplies for bikes in a two-drawer toolbox which I can keep near the bikes in the garage or take with me as needed.