Pomegranate: juice is used in Strengthening Solution. (Yeah, I know, that pom is past it's prime. I found it in the back of the fridge)
Phlox: used to attract flocks of birds to a garden, which then eat the bugs.
Shamrock: used in Ireland as an ingredient of Good Luck potions.
Muscari: Essence of muscari can be used as food coloring, but too much causes the ingester to turn violet. It was almost revealed to the Muggles when the affect was used in the making of the movie “Willie Wonka and the Chocolate Factory” Luckily the film was charmed, so Muggle viewers believe the affect to be just a bit of movie special affects.
Leaves of a bubotuber plant. The pus of the tubers themselves (found underground) is used to treat acne.