Not all plant diseases "build up" in the soil, and some (e.g., botrytis blight http://bit.ly/Zi0oWz; powdery mildew http://bit.ly/Zi0Pjv) affect such a wide range of plants that rotation alone won't solve the problem.
Best ways to prevent diseases in any crop: learn as much as possible about the diseases prevalent in your area, look for resistant varieties as Rachel says, check plants often for signs of disease (then rogue out the sick ones if possible), and--very important--remove all diseased plant tissue from your garden. Don't compost it! Bag it and put it out with the trash, or bury it somewhere far from the garden,
Late blight is a special case. If it hits your area, it's almost impossible to protect your tomatoes and potatoes without fungicides. Organic growers can use fixed copper or Bacillus subtilis http://bit.ly/Zi1JfP, which generally work only as preventatives, not once a plant has been infected.
Note: I've found Little Leaf cucumber highly resistant to powdery mildew and other cucurbit diseases. It's a compact plant (good for containers), but produces heavy yields of good-sized pickling cukes. Also resists those awful cucumber beetles.
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