Every Maker, Hacker, Scientist, or just plain Tinkerer needs a work space in order to achieve world domination.....Or... Well...er.....I Mean work productively. This can be a Basement, a Shed, or my personal favorite, the Garage Lair. This is not meant to be a strict set of rules, for your needs may vary whether you're a welder or an electrical engineer or a chemist.
Step 1: Plan on what you need.
I do a mix of machining, welding, fabricating, woodworking, soldering, and chemistry. Thankfully, my shop has the tools to accomidate a decent tinkerer. There is a spot in my shop for each tool or group of tools. Also invest in a wall of parts bin to keep everything organized. For instance, the wall of crates I have are each delegated a certain group of parts or supplies ( i.e. Rockets in one box, Explosive mixes in the other, Tapes in another, Screws and fasteners in another, etc..)
Step 2: Small Parts
It helps to have a rack of small containers where each one is no bigger than a credit card. These will store those little evil pieces that always seem to get lost on the ground. ' Tis the bane of my existence in the garage! But if you loose that teeny tiny resistor, it's not like one can cope without it. Just trust me, the 15 dollars put into it could save you hours of commute to and from the local Radio Shack.
Step 3: The Safety Aspect
Or.. well... somewhere up there in the list of priorities.
Gloves and eye protection are a must. You can buy some quality gloves for $10, but you can't buy fingers. Second to our hands, our eyes are the most sensitive part of our bodies. If iron dust from a grinder gets on your cornea, it will be a world of pain. Just trust me. Like I said before, your needs can vary. If you are a solderer, buy a CPU fan to keep out fumes, If you weld, professional welding gloves will help.
Fire is also a big risk to any pyromaniac, **Cough**Tetranitrate**Cough**, so at least one extinguisher is paramount.