I want to raise my chickens mostly organically. I don't feed them organic food, but I want to take an "integrated pest management" approach to treating problems they have. Integrated pest management consists of implementing preventative measures first, and then if a problem arises, using the least toxic methods first. Whenever a bird becomes sick, the first thing you should do is separate it from the rest of the flock, so that the sickness doesn't spread. Here is an overview of common diseases.
A Clean Environment
Cleanliness is the most important prevention for disease and parasites. Quarantine new birds for a month before adding them to the existing flock. Better yet, start with and introduce only day-olds on your property. Keep the coop floor dry and smells down. Keep food sources clean, do not feed chickens spoiled food, and store feed in a dry place.
Moldy food can cause vent gleet. To cure vent gleet, use copper sulfate; and then probiotics when the bird no longer has diarrhea. A bout of vent gleet compromises their internal flora and makes it more likely they'll get it again, which is why you need the probiotics after the treatment.
Probiotics are used to prevent bacterial and fungal infection of your birds' digestive tracts. They can significantly reduce the need for antibiotics. Here's an article about preventively avoiding the use of antibiotics with probiotics: Raising Drug-Free Poultry. I currently add 1/2 tsp dried garlic and 4 Tbsp livestock probiotic or yogurt per gallon of my birds' water.
DE is used for many things, including protection of food and grain from insects, internal and external parasite prevention and reduction, and basic regulation of the digestive tract. It works by dessicating and piercing the pest, and like fiber to hold together feces. Eggs and meat are safe to eat from birds fed DE, but you must use only food-grade DE. DE for pools and gardens is unsafe for any animal to consume.
The cheapest sources I have found for it on the web are Perma-Guard and Custom Milling. In western Washington, you can get it at Bill's Country Farm and Feed in Enumclaw; Dels in Bellingham, Chehalis and Port Orchard; and you can also special order it at many other feed stores. Under $20 for 50 lbs is a good deal.
If your chickens get diarrhea, it's a good idea to take some of their feces to a vet and get them tested for parasites. As diarrhea can be caused by many things, don't use a wormer unless you know your birds have worms. Overuse of wormers is what causes worms to become resistant to wormers and wormers to become useless. You may want to try DE first before a wormer because you also will not be able to sell or eat the eggs during worming and at least a week afterwards. Here's a great article about worms: Intestinal Worms.
I have been reading chicken health books, and by far the best I've found is The Chicken Health Handbook by Gail Damerow.