Most workshops in Dwarf fortress are represented by 9 squares in a 3 by 3 square pattern. Some are 5 by 5 (Siege workshop), or 1 by 1 (Quern, Screw press, and Millstone). Getting a proper work flow is very important to the success and wealth of your fortress.
Laying out your workshops in the most efficient way possible is quite a science. There are several points that should be considered.
Keeping workshops of a specific industry together is a great way to see if you need more workers creating booze or making leather toys. If you have all of the food related workshops in a single room, you can tell with a glance that your cooks are slacking off.
Just as you want your looms close to your clothier's shops, and you want your tanner's shop next to your butcher's shop, you will want logical stockpiles close to your workshops. It makes sense to put your raw food stockpile right next to the kitchen, so that your cook doesn't spend all of his time walking from one end of the fortress to the other. If the correct stockpile is close at hand, those roasts will be coming out of that kitchen in no time.
 Using stocks
When a dwarf claims a workshop for his very own, you have a 50/50 chance of the artifact he's about to make being really awesome. He could make an artifact throne out of three lumps of bituminous coal, and it will be worth a whopping 4800 dwarf bucks. However, if you forbid every stone in your fortress except for the natural platinum, he'll make you something very near a six figure artifact.
There are a few ways to control what he chooses. A start is to have the workshop that he claimed be in a room that is only reachable through a door. As soon as he claims it, lock the door so that he'll just sit there yelling out the things he needs. Now you can go on making only the items available you want him to use (usually the most expensive). You can forbid unwanted items both from the stocks (may require highest precision achieved by your bookkeeper, especially for stones) or after he has collected them (will retask search for that item), dump items inside the workshop or near the door(the later won't work if he has a preference). If you use mass-forbid take good care to allow everything after the artifact is finished!
 Artifact Construction Complex
Alternative solution is to build Artifact Construction Complex, containing every mood-able workshop and small stockpiles of most precious types of ore, metal bars, gems, etc. When not in use, ACC should be either locked, or everything in it forbidden (including workshops). Forbidding is better, because in this case these workshops won't receive orders from your Manager. You can also deal with it by filling workshop's job queue with 10 suspended jobs. Once the dwarf is struck by the mood, ACC is opened, and all claimable workshops not belonging to ACC is forbidden.
This way the normal operation of the workshops is disrupted only for the time needed for moody dwarf to claim workshop, instead of all artifact construction time in first method. Further more, only one type of workshop is nonoperational, instead of all workshops that use forbidden materials.
When the very worst happens and your triple legendary dwarf fails his strange mood and goes on a rampage destroying the faces of all the pets and dwarfs around him, it's good to be prepared.
The easiest form of protection is a simple door on the room the workshop is in. Lock for the few months it takes for him to die of thirst. You can spend the time waiting for him to die by getting his coffin made and situated.