Every time I play OoT, I always have one Magic Bean left over. Here's a list of the one's i've collected thus far:
Gerudo Valley
Zora's Waterfall
Lost Woods (2)
Kokiri Forest
Lake Hylia
Death Mountain Trail (entrance to Dodongo's Cavern)
Graveyard
Spirit Temple (entrance)
You don't need to plant the one outside Dodongo's Cavern, you can backflip off the place where you throw the bomb flower and land next to the heart piece
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Belief or disbelief rests with you. To die without leaving a corpse... that is the way of us Garo
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