Sure, some of these areas have nothing valuable ...but who cares?
They're secret...
Golden Rupees (200):
As Adult Link, on the highest floor in Goron City, is an area
of lava. You need the Longshot to make it across...at the other
side is a chest with your Golden Prize! I know, it's out in the
open, but it's really easy to overlook.
Before the entrance to Goron City is a platform with a circle
of rocks on it. Simply stand near it and play the Song of Storms,
a hole will open up. Inside is a cave with a chest. Guess what's
inside?
In Kakariko Village, in front of the tree at the entrance,
is an area where you Stone of Agony will shake. Bomb it and then
go inside, kill the enemies, then claim your prize! For those
of you without the Rumble Pak, coming from Hyrule, just keep going
forward, pass the tree, then lay bombs in that general area.
In the Gerudo Training Grounds, in the room where you receive
Key # 2 (see Gerudo Training Center section). Defeat all the Like
Likes and a chest will appear...guess what's inside?
In the Fire Temple, go past the room with a moving fire pillar
so you're on the upper most level of the boulder maze. Look to
your right and up and play The Scarecrow's Song to lure Pierre
out of the shadows. Use him as a Hookshot target. Once there,
turn around and use the target there. Climb the vines and you'll
be in a room with a switch. Trigger it, then quickly run, use
the Hookshot target to pass the hill, and open the chest before
the flames come back. Dun dun! Golden Rupee. You can also find
two Golden Skulltulas along the way.
In the room where you originally find the Lens of Truth...use
the Lens of Truth and you'll find a small chest with a Golden
Rupee inside!
In Goron City, highest ledge, is a room with a lot of rocks
that form a maze (see below). Now, if you have the Megaton Hammer
you can clear out the long line of red boulders. At the end is
a lonely chest with a Golden Rupee!
Purple Rupees (50):
Near the entrance to Goron City is a strange "skin"
on the wall, it looks like a drumskin almost. It's a little before
the area with the circle of rocks. Bomb it, it's covering an aclove
with a chest. Inside is a Purple Rupee!
In Goron City, bomb the rocks on the upper level and follow
that path. Now we're in a maze of sorts. There's a whole slew
of goodies in here, including two chests, EACH holding a Purple
Rupee.
Gerudo Valley, there is a circle of boulders. Destroy them
with the Megaton Hammer, inside is a chest with a...dun dun...Purple
Rupee!
Catch the Hylian Loach and show it to the fisherman. He appears
if you enter the pond the second the cucco crows in the morning.
Check the Secrets Section for more details on this.
In Gerudo's Valley, as an Adult, is a ring of boulders along
the wall. Pulverize them all and it will be revealed that they
were concealing a chest. Guess what's inside...no, not something
evil...
In the Haunted Wasteland, go to the rock platform where you
meet the ghostly guide. On the side of it is a hole, go down it.
Besides a Golden Skulltula, you'll find two torches. Light them
using a Fire Arrow or Din's Fire and a chest will drop down, inside
is an easy 50 Rupees.
Misc.:
Near the top of Death Mountain is a boulder, blow it away.
Inside the hole that is under it is a cow, and some Rupees.
Go to your extreme right after exiting the Market. Blow up
the boulder there and fall down. You can find a Blue Rupee (5),
among other things.
Go to your extreme left after exiting the Market. Blow up
the tree and fall down the hole. Besides the Golden Skulltula,
you'll find some Rupees.
In Kakariko Village, as an Adult, go into the normal Potion
Shop, it's near the entrance to Death Mountain. Inside is a door
to the fenced off area! This is not accessible as a child (unless
you use a chicken to glide over the fence). Behind there is a
Secret Potion Shop that sells Ultimate Blue Potion, which will
re-ill all your hearts and your magic meter. It may cost 100 Rupees,
but it's worth it! Don't go into any dungeon with out it.
In the same place is a hole, down it is a chest with some
Rupees. Also, try catching a fish that is in the little pond.
In Goron City, bomb the rocks on the level where the rolling
Goron is to find the giant Goron. As an Adult, he'll see you the
Giant's Knife. It's very powerful, but it breaks after a few hits.
The Big Goron's Sword can fix that...If you're wondering, the
Giant's Knife costs 200 Rupees! Ouch!
After getting the Silver Gauntlets, you can lift the gray
rocks that are scattered around Hyrule, and you might find something
of interest underneath them! For example, on a ledge in Gerudo
Valley is a stone of this kind, and under it is a cavern with
about 50 Rupees. Search around...
Another gray rock is found at the entrance to the Spirit Temple.
Underneathe, Deku Scrubs will sell you Red and Green Potion.
In the Graveyard, in the Royal Family's Tomb, light the two
torches in the first room to get some bombs.
In south east Hyrule Field is a boulder in a grove of trees,
blow it away for some easy Rupees.
Hyrule Field again. Near the fenced in area right near the
entrance to Lake Hylia is a hole...No bombs required, it's right
in the open. Inside Is a chest with a blue Rupee.
Lake Hylia! On a small island is a tombstone, pull it back
to reveal a hole. Inside are several Deku Salesmen.
Lost Woods...Near the Warp Point to Goron City is a boulder,
use some bombs and go down the hole. Can you say Rupees?