Tips for Setting up Shop
The Heart of the Shop
At the center of my shop, not surprisingly, is my workbench and my table saw. Being a Galloot, I spend more than half my time working at my workbench. The integrated cabinet stores the hand tools that I use most so that they are readily available. Longer items, like by rules and straightedges, are stored nearby on my pegboard. My workbench started out almost verbatim as the one in Danny Proulx's book "Building Workshop Workstations", but has gone through several modifications as I figured out what I really needed in a workbench.
Also in the center of my shop, just to the right of my workbench, is my table saw. Having the table saw near the center of the shop give my clearance for cutting long stock and sheet materials.
Tips for Setting up Shop
I feel that I have finally optimized my shop setup for the tools I have, the way I work, and the space that I have. Although it has and will continue to evolve, it has not changed significantly for a few years now. Perhaps that is a clue that I have finally gotten it right. Here are a few tips that I have incorporated:
Keep horizontal surfaces at the same height: Having my workbench, my table saw, and my auxiliary workbench at the same height are the more obvious examples, but also look for some less obvious opportunities. The bed of my lathe, located in front of my table saw, is also the same height as my table saw and serves as infeed support for long stock and sheet materials. My cabinet for my drill press is also the same height as my table saw and is on wheels, so I can "borrow" it if I need additional infeed or outfeed support. If your shop is in a garage like mine, be aware that the floor is likely sloped, with a gradual downhill towards the garage door. This is mostly a nuisance, since it makes more work of leveling workspaces and must be taken into consideration when locating a workstation that is to be the same height as another, but it came in handy for me since my lathe bed is actually slightly taller than my table saw. By installing it down hill, closer to the garage door, I was able to make the lathe bed and the table saw on the same plane. 
Most "mobile" machines can actually be "semi-mobile": When I first discovered the virtue of having machines mobile, I went a little—uh, way overboard. Some days it seemed as though I spent more time shuffling machines around than I spent on working wood. I have since backed off from having everything mobile,
and now my machines and workstations seem to have fallen into three categories regarding mobility: Stationary workstations, like my workbench, and table saw which I use constantly and are not easily made mobile; Semi-mobile workstations like my planer and drum sander on my "milling wall", which mostly need only be moved a small distance to make clearance for it or another nearby machine, or to simple "get it out of the way" (this constitutes most of my mobile machines); and finally mobile workstations that may move around quite a bit, like my assembly table and miter saw. Of course, the extent to which you should make machines mobile will depend on how much space you have in your shop, and whether some of that space is temporary, for instance, a garage shop that has to share space with a car. In general, however, I find that the more machines that I can afford to keep stationary or semi-mobile, the better. - Build workstations with integrated storage: This is the old adage "a place for everything and everything it it place" as applied to a woodshop. What better
place is there for drill bits than in a drill press cabinet that fits under the drill press table? or for lathe tools than a lathe cabinet mounted under a lathe bed? Now I know this may be a bit of a tall order and a long term commitment for folks just starting to set up shop, but it is probably the number one thing that keeps my shop organized and efficient. - Consider Melamine for workstations and storage: Since I do not (did not) want to spend a large part of my early years of woodworking building shop workstations and storage, I
decided to make most of my workstations from Melamine coated particle board. It is strong enough for shop use, affordable, and relatively fast and easy to construct. I prefer having drawers and cabinets as opposed to open shelving because it keeps the stowed tools and supplies clean. There is a wide variety of affordable drawer slides and hinges available for use with Melamine. - Plan for enough of workspace: When I initially setup shop, I had but a 2' x 7' table for a
workbench. This proved quite inadequate. I now have a workbench, assembly table, auxiliary workbench, and the bench where I currently do my sharpening. I use all of this space, and sometimes even use my table saw as an additional workspace.