Summary
The most important aspects of thrush treatment is prevention. If the environmental factors that favor the development of thrush are not managed, then it is likely to continue to be a problem despite treatment.
Stalls or stables should be kept as clean and dry as possible. Stabled horses should have their feet picked out 1-2 times daily, with special attention paid to cleaning out the grooves in the center of and on either side of the frog and removal of any dead tissue and black material.
Ideally, horses should have consistent exercise and should not stand around all day. Exercise keeps the feet healthier and cleaner. This keeps the grooves more open to air, reducing the development of thrush. Routine, scheduled hoof care with appropriate trimming and removal of dead frog and underrun sole is recommended.
There is great competition between commercial thrush treatments. In truth, just about any antiseptic will easily kill thrush bacteria - dilute bleach, hydrogen peroxide, copper sulfate, iodine products, even topical antibiotics. Fresh air alone also kills the organism, if it is allowed to reach it. However, treatments (commercial or homemade) will not help if the grooves are not first well cleaned or if any dead tissue remains.
My preference for treating thrush is an iodine/sugar mixture or copper sulfate, a drying agent, applied only after cleaning and removal of all dead tissue. I use a hoof pick and knife to remove the majority of the material and a small stiff brush to clean out these grooves. Only then should topical treatments be used. (Note: I personally do not use wire brushes because pieces of wire can become embedded in hooves.)
Your vet should always be involved in the management of thrush when accompanied by lameness, when the grooves are very deep, or if thrush is not responding to basic treatment.
Any lameness or other illness should always be promptly diagnosed and treated. Lameness can contribute to the development of thrush.