Throughout Ocarina of Time's Hyrule are 10 soil patches that Magic Beans can be planted in.
They are covered in order of appearance.
TODO: add pictures
To the east of the Kokiri Item Shop, between the roots and wall.
From the entrance, go left twice.
From the entrance: right, left, right, left, left. (E, N, E, N, W) It's behind the Business Scrub on the right.
Enter the graveyard proper and go up the hill to the left (north). It will be on your left at the base of the nearby ledge.
Immediately in front of the entrance to Dodongo's Cavern.
Adjacent to the man selling Magic Beans.
On the northern side of the Lakeside Laboratory.
Take a Cucco to go into the gorge, toward the waterfall. The patch is next to the Gerudo woman, box, and cow at the bottom.
Near the Bolero of Fire warp point.
TIP: Don't go to the Crater as Child Link unless your health is full! The time you have in the Crater is based on your current life: 4 seconds per quarter-heart (16 per heart). Bring a Fairy if you have fewer than 10 hearts.
In front of the Colossus.
Here's a quick checklist to keep track for yourself: