In general, many of your vitamins can be taken together. However, always check the label directions to ensure there are no specific interactions.
One such example is calcium and iron, which should not be taken together (as calcium inhibits iron absorption). Also check the label directions to see if any of your vitamins need to be taken with food or on an empty stomach – in which case you may need to take them separately.
In terms of medications, while some supplements actually assist in making up for nutrients that can be depleted while taking prescription drugs (statin drugs taken with CoQ10, for example), your doctor can guide you on what to take when to ensure maximum safety and absorption.