There are no rules about the best time of day to take supplements. My advice is to take them when they agree with you most. Many people find taking pills of any kind as part of a morning routine makes it easier to remember, so taking them with breakfast is a popular option. Vitamins and mineral supplements can cause nausea, heartburn, and other gastric disturbances, especially when taken on an empty stomach. For best absorption and the least irritation to the stomach, I generally suggest taking your supplements with a meal containing fat. This is particularly important for the fat-soluble vitamins (A, D and E). Experiment with taking your supplements with lunch or dinner, if they cause you problems with breakfast.
Foods - or an empty stomach - can also interfere with absorption of some vitamins and mineral supplements. With calcium, for instance, you need enough stomach acid to assimilate it so you're better off taking it after you've eaten, because food in the stomach stimulates acid secretion. Tannins in tea can block absorption of iron, while vitamin C enhances iron absorption, as do fermented soy foods such as miso and the lactic acid in both yogurt and sauerkraut. Other foods that interfere with iron absorption include caffeinated beverages, eggs, milk and bran. (You shouldn't be taking iron supplements or a multivitamin/mineral containing iron unless you're a premenopausal woman with a heavy menstrual flow or your doctor has recommended an iron supplement because a test has shown that you're iron deficient). In addition to these foods, excess consumption of alcohol can interfere with absorption of several vitamins and mineral supplements.
If you're eating a healthy, balanced diet, however, you have no reason to worry about foods interfering with the absorption of your vitamins and mineral supplements.
Andrew Weil, M.D.Visit Dr. Weil's Vitamin Library for comprehensive information on vitamins and mineral supplements.