This is a question that comes up at least once a month in the jewelry making forums. Everyone has a bit of a different way it works for them. Somethings seem pretty universal after trial and error most people end up doing a few things the same.
Lighting is important. I have two lights and then an over head on the ceiling. As I get older I think I might need a flood light too! The two lamps have daylight bulbs so I can see the colors I am working with as true as possible.
I didn't even clean up before I started this article. I thought about it but then changed my mind. This is how it looks all of the time. It may be creatively messy but it is organized. Well okay sometimes it looks even a bit more chaotic.
Beside my desk and my chair I have a book shelf. On the end I have hung nails and on each hook I hang all the gemstones of a certain color together. When I use some beads on a strand I just knot the strand again with the left over gemstones and hang it back on it's hook. I like this set up since then I can take the bead or pendant I am trying to match up and I can just run it past all the colors to see what works.
On the upper right corner you can see my two tins where I store my silver and copper scraps. I always plan to someday use them but the pile just seems to keep growing. 
The same shelf to the right of my work bench holds the jewelry I recently made so I can look at it over a few days and see if I want to keep it as is or change anything. Eventually it goes into cases.
This is the same view of the recently finished pieces from my chair at the work bench.
On top and to the back of my work bench I put up this shelf that I can bang nails into to hang beads and my dremel. I also place finished jewelry there to inspire me and to look at them to see if I want to keep them as they are. I find I don't store much on the higher shelves since I can't reach it from my chair so it never gets back up there.
My drawers hide the real mess. 
The next drawer down holds all my base metal wire. Presenty all I have is copper, brass, steal, memory wire and a bit of colored artistic wire.
The drawer to my left holds everything that defys organization. Files, glue, markers, paste, wax, you get the idea.
The bottom drawer to my left houses all my sterling in big gallon baggies. Each is labeled by size and shape. I flop open the part I am working on and then when I am done with that bag I toss it into the opening. This system works better for me that using a file holder since I found I wouldn't get them back into the right spot. With this I do every time. I sort by shape (silver round) from smallest to largest. Then 1/2 round, then square. I also keep my shaped brass and copper in the back of the drawer organized the same way.
To the left of my bench is another shelving unit with even more nails to hang beads. When I get into making a piece I find I need to see as many beads as possible to really get the ideas rolling.
The shelf to my right holds my beads that have no strings or are pendants. My daughter helped me label them. I love her hand writing :) 
A close up of my "need to finish this" pile of boxes.
Close up of my wire graveyard.
On my desk and to the left I found this wire shelf (I stole it from my sister). It is iron and perfect for hanging my pliers, hammers etc from. The shelves store big and odd things like my tumbler, paint brushes, mandrels etc.
My pliers. I love my lindstroms. Before I bought them I worried I would have to stop working with wire because of the pain in my hands. I have not had that problem since I started working with them.
Out of that mess sometimes comes beauty. That is the most amazing thing I think.
