I've been taking my vitamins, minerals and a few herbal supplements for many years, but I've always wondered about the right time of the day to take them, and how to best ensure that they get the optimum absorption in the stomach. In the last couple of years, I've moved from taking a big handful of supplements with breakfast to spacing them out a bit during the day, based upon what they need to have along with them when they go down.
As a general guideline, vitamins go best with food. To avoid any queasiness and to ensure they get absorbed, your "with breakfast" routine isn't bad -- or even better, with the largest meal of the day. But if you are taking a number of vitamins and minerals, it's better to space them out a bit over all three meals.
There are certain vitamins like A, D, E and K that are fat-soluble, and these are the ones you take with food, because they need some fat in order to get into your system. Other vitamins, like the B and C vitamins, are water-soluble and they can be taken at any time of the day, with or without food. Omega 3 capsules and fish oils need to be taken with food, as does CoQ10.
When I take my Arctic Root® in the morning, or any herb, I either take it 30 minutes before breakfast or 2 hours after any meal. Herbs are much more sensitive and shouldn't be taken along with a meal, because they often get washed into the digestive tract along with the food and you lose much of their effect. Other supplements that can be taken with herbs, and not with food are probiotics and "green" supplements.