You can also try to ward off Botrytis by spraying with copper fungicide early in the season before the humid, foggy weather starts. In the same article, Diann Putland suggests using Bordeaux before the lilies emerge, but she warns that "as a foliar spray Bordeaux may not be acceptable to a grower who wants to show stems as it will stain the foliage. In that case Benlate, also known as Benomyl, a systemic fungicide, may be the best chemical to stop a infection after it has started. Spray the plants when the foliage is dry and be certain to apply spray to the underside of the leaves."
The other major disease affecting lilies is Lily Virus, which is spread by aphids. Lily Virus will not only cause your lilies to look bad (as it causes twisted, distorted growth), but will reduce their vigour. According to Diann Putland, the leading symptom of Lily Virus is streaking of the foliage caused by the reduction of chlorophyll; infected plants need to be removed immediately to reduce the chances of aphids carrying the disease to other healthy plants. 1001 Hints and Tips For Your Garden recommends controlling aphids by watering a systematic insecticide into the soil or spraying plants with rotenone (p. 169).
Personally, I always try to avoid chemical controls whenever possible; I control aphids in my garden by hand-picking them and by squirting them with a homemade spray of dishsoap and water. The best control of all is a thriving ladybug population; it's pleasant and easy. You can buy packages of ladybugs now at many garden centres if your local population doesn't seem to be thriving. (Remember; your local ladybug population will do much better if you don't kill off their larvae, which look like little dinosaur beetles.)