IKEA makes these great little wooden chest-of-drawers things- nine drawers, about 12" by 15" by 9". Quite cheap, great for organizing little bits.
Also check hardware stores for the little plastic tray cabinets.
Get a good toolbox. For commonly used tools, consider pegboard on the wall behind the desk, or magnetic knife holders that mount to the wall, or super glue a magnet to your tools and put a metal sheet up somewhere.