I've had a reasonably hard time sorting and finding things for projects in the past, specifically electronics projects, but recently I have found a ragtag bunch of containers and organization methods that work for me. I will add to this Instructable as new things come up.
Below is some scattered stuff from around my work area. Many of the large objects just go in bins or in a drawer, but the smaller ones are perfect for this system.
Step 1: Paper Clips As Wire Holders
Un-bending paperclips and wrapping them around wires holds them in place. You could use a zip-tie, but you have to cut them off and thus, not reusable.
Step 2: Yogurt Cups
Make good use of those empty yogurt cups. They're great for screws, springs, and other stuff.
Step 3: Cheese Containers
The containers that cheese sometimes come in make great trays to use to help you keep parts separate, or so you do not lose parts when disassembling something.