Put everything you can on casters... Every piece of equipment I own is on casters. Doing this makes for a very mobile, easy to clean and adaptable workshop. I have one bench that is stationary and I use that very little. My tool post for the tubing bender bolts to the floor but that is hard to get around to keep it solid.
Lots of light is very important as Don said.
I have gotten away from shelves and pegboard as much as possible though. They collect to much dust and dirt and I replaced most of that stuff during my shop makeover with some plastic wall cabinets from Home Depot and a few yard sale cabinets and drawer units. Watch the yard sales for this kind of stuff. I bought my kitchen wall cabinets for 2 bucks apiece...
Mark