In this page, I'll list the location of all the dirt patches where you can plant a bean as a kid, and where they will take you when you are an adult. The bean selling guy is located in Zora's River, and he will keep increasing the price of the beans as you buy them. 100 rupees is his limit. Keep in mind that you can re-use the bottle of bugs if you swing your bottle right after releasing them to get them again. Cool trick!
Hole One
Hole Two
Hole Three
Hole Four
Hole Five
Hole Six
Hole Seven
Hole Eight
Hole Nine
Hole Ten
This hole is the first you will encounter. It is located in Kokiri Forest, right by the Kokiri Shop. Plant a bean and release a bottle of bugs in the hole for a skulltula as a kid. If you ride the bean as an adult, it will take you all around Kokiri Forest.
This hole is located in the Lost Woods if you head left, then left again. You can get a skulltula from this one as well. When you ride it, it will take you through the area over the bridge, and is especially useful when trying the cut time doing the trading sequence for the Biggoron's sword.
This next hole is located in the lost woods as well. Head right, left, right, left, forward, left, left (or strait). The hole is located behind the Business Scrub. The hole will give you a skulltula, and when ridden as an adult, will lead you to a skulltula on the ridge above.
This next hole is in Kakariko Graveyard. If you head North-West from the entrance, you will find it. The hole will give you a skulltula, in addition to taking you to the top of the edge which will give you a heart piece.
If you find the bean seller, look right beside him for the next dirt patch. This hole will not give you a skulltula, but will give you a ride to the bridge heading to Zora's Domain. This is really useful when you want to get somewhere in a hurry and you haven't the patience to go the long way.
This hole is located right by the entrance to Dodongo's Cavern. In addition to giving you a skulltula, when ridden, it will give you a lift to the top of the cave entrance which contains a heart piece. There is a way to get the heart piece without the magic bean - do a backflip from above where the fence is cut slightly shorter where the bomb flower is.
This hole is located next to the warp point in Death Mountain Crater. This hole will give you a skulltula and a ride to the top of a rocky point which hides a heart piece.
This hole is located right by the Spirit Temple in Dessert Colossus. Right by the entrance to the temple is the hole. It will give you a skulltula and a ride around the area. If you jump on the rock formatio, you will find a heart piece. If you jump onto a huge rock during nighttime, you will find a skulltula.
This hole is located in Gerudo Valley. If you head right from the beginnning of the bridge and jump, you will land on a ridge and find the hole under the crate by the cow. This will give you a skulltula and a ride around the valley, it will not take you back up.
The last hole is located by Lake Hylia. This hole will take you to the roof of the laboratory, where you will find a heart piece at the very top. If will also give you a ride to the fishing pond. If you have not yet completed the Water Temple as an adult, you can still reach the fishing pond by means of the magic bean. Oh yeah, it will also give you a golden skulltula.