Great topic! I know a few, but not nearly enough. Here's my wee contribution.
Garlic (freeze-dried or fresh) should be taken away from most herbs. Other forms of garlic have very little or no allicin content remaining, so isolating it isn't really neccesary.
Zinc for immune support is most effective taken in a 10:1 ratio with copper at the same sitting
CoQ10 for best absorption should be consumed with some fat
Cilantro (fresh) for detoxing is most potent eaten shortly before bed with food
Sam-E for cognitive/mood support is most potent taken on an empty stomach
Chlorella is a more potent detoxer taken on an empty stomach exactly 30 minutes before meals