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Night Mode: As the name suggests, your game will always be at night when this code is enabled.  Helpful for spotting those elusive treasure halos and Chu-Chu's.

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Advance Time: This code supposedly advances the progress of time.  However, it more likely performs some sort of color cycle, as it makes all of the colors change.  It can get really funky, too... try it out, just for kicks!

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Bottle Codes: The following codes will modify the contents of your bottles.  The first column describes the contents of the bottle, and the following four columns are the codes to set those contents to the respective bottle.

Empty
47TP-2YEE-2H595
U370-81GJ-AWJCR
3HP3-AMHC-94QP7
ER60-X6N5-EFJ2J
C3PX-9PM1-PQWXB
CF82-XBPU-EP7P7
RHHR-5X4X-JEX9J
6RRM-GA8W-VCEXM
Red Potion
R2X8-XP7J-BWRRF
011K-2XZ5-A8XTE
9X52-W32M-8UKN2
GBHK-F9J5-Q10ZW
918E-TTGZ-4PCZ0
WRFT-714K-21JFY
1675-GFY1-2ZZQN
3WWW-74XU-T0R5W
Green Potion
0MFF-APE2-H2V4D
D863-V32R-732JG
5QJ2-CA0X-H1306
5YTR-MYP0-6TPRC
E9Q9-QKBA-GNHF4
52JN-8K1E-DCB6J
T0YX-BVEN-J4YXT
XW9K-8TVA-A6BVW
Blue Potion
PWPQ-MCZJ-P418F
ZG77-DUG9-5M9HZ
THPV-PFX9-CCRTX
VYQR-5WB2-U3WRU
J9RR-1EXM-1ZXTB
JT28-3N4R-BH6FY
N6J8-0NKW-QVAX4
TFE9-U509-UA3YY
Elixer Soup (Half)
AQP9-PRA6-NDVG8
31T8-A5MZ-E4U2V
RK7W-2AKY-XTPHG
A04N-D9HW-5AV1P
WU8F-8Z9K-NGFYQ
ZVYF-2BZ6-PFH07
EHEU-6CQY-ZYTXN
JPNR-TWJZ-EJECD
Elixer Soup (Full)
QJUM-5CKT-2AEK9
3U9D-3XWY-4DWZU
A7CD-MUED-VNF7Z
XHQK-U5MR-G9MYT
5W9A-2WDD-JHDMQ
ZFK6-4U1B-Z5P63
W53E-3XZN-Y8KEG
XC80-K6DY-YHPYC
Water
H950-ECN7-RUPBA
BRUD-H8QP-8GRDR
9WZG-V82T-WJH2F
BKD8-5CQW-NE7Y9
GT1N-6FM6-WRQFT
FHDH-7WWD-JQXDY
7Z9Q-9XTX-VEPKJ
BD9C-HRNK-U7VXJ
Fairy
8QF3-8D1J-21JYM
YXE8-PXZ9-V7D9Y
7JUA-A4WB-NFGH8
DK6D-1ABV-34C8G
7MAD-Z1QP-0H6KA
XE0K-BE2E-7AFAE
QX5W-UH07-40H74
2GGY-8CED-91MPC
Forest Firefly
96TY-5008-KHRNH
N0U4-TPYH-4FRPU
J0HV-5A79-RJ1RX
8R29-EHBK-FGNMN
5QNR-19ZK-90TUF
55MY-2NFN-R0UF0
8NT5-N43M-W7DRQ
YBHE-PQ70-X9TNH

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Spoils Bag Codes: The following codes will modify the contents of your spoils bag.  The tables are arranged in the same order as the bag.  All of the codes will provide you an infinite supply.

GRQM-UKHE-CN2Y5
CDMJ-K3CQ-U8KMB
J0EC-DHYV-T2VQ6
AZK4-NNEN-GRTGF
TGTW-JMYB-XAU71
QAWH-W767-3G8MR
RM93-C87A-MW9W0
AZ5K-CVA8-8FY6F
DFE5-BPZ4-B6RG5
E2V7-V5PD-M2ZE6
XMZW-0AXD-9CXA1
6UGX-D3VU-VM67B
VH15-KCX9-9RQDD
WPX0-JE2A-9HH8N
6031-D4VP-T1QGW
KMQ0-4M6Z-WHFPB
PXKX-T7FC-XUNVH
P7Q4-G9Y8-T6K2M
6JH6-5C0B-BJ48Q
BKGR-J998-C5JRQ
R45T-6C47-GRBK8
ZDP7-6049-27C1X
0MKY-W7T9-4EBJ4
3QZU-MM5P-2T82P

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Bait Bag Codes: The following codes will modify the contents of your bait bag.

Infinite All-Purpose Bait
Infinite Hyoi Pears
HV0A-XQ23-TEBEP
0CUT-WYYP-5VWNC
AM4T-6W19-N8TPF
2VZK-7GVY-U49G3
PP5Y-PFHV-FJ5YB
VDHP-ANKT-6X6TJ

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Delivery Bag Codes: The following codes will modify the contents of your delivery bag.  The tables are arranged in the same order as the bag.

No codes are available for the delivery bag at this time.

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Japanese Text Item: I'm going to get a screenshot of this item as soon as possible.  I'll also translate it, so we'll know what the mystery item is and what it does.

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Down for Tunic, Up for Hookshot: I have no idea what this is supposed to mean.  I'll try out the code as soon as possible.

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Hero's Charm Code: This is the Hero's Charm, not Tetra's stone!  You know, the weird mask that shows an enemy's HP?  Anyway, if you save your game with this code set to On, you will not be able to remove the mask.  If you save your game with this code set to Off, you will not be able to put on the mask.  If you remove the activator codes (you'll have to either decrypt the code first or take a random guess and remove lines), then the mask will rapidly flash on and off and the enemy's health bar will be semi-transparent.  Saving will either force it on or off, depending on whether the mask was on when you saved.

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Fully-Charged Master Sword: I'm going to play around with this code and see what it does, exactly.  It doesn't make much sense the way the title describes it.  Also, according to the sources, you must have the Master Sword.  Not sure why.

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Jump: Umm... I'll have to test this one.  It sounds weird... and apparently you're supposed to keep the number of codes activated down whenever you use this code.

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Mega-Jump: Umm... I'll have to test this one too.  You're also supposed to keep the number of codes activated down whenever you use this code as well.

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Submarine: If you attempt to exit the submarine, the game will freeze, since the game has no idea which submarine you were supposedly in.  This is similar to the "Grotto Glitch" one would encounter in the Beta Quest for Zelda: Ocarina of Time, where exiting a grotto while in the Beta Quest would freeze the game, since it was not sure where to send Link to.

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Ice Island and Fire Island: If you attempt to "enter" Ice Island or Fire Island's caves without melting or freezing them (respectively), then you'll immediately be warped out.  Be careful!  Please note that if you've beaten either of these islands, then you won't have to worry about melting or freezing them.

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Boating Course: If you use this code, please be warned that you will be unable to exit the boating course or the game.

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Sturgeon's House: Oddly enough, if you use this code, you will be inside Orca's part of the house.  Doesn't make much sense, does it?

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The Sea: This code will place you in the sea near Outset Island.  Weird, huh?

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Beta Triangle Island: If you use this code and then head to the Tower of the Gods, you'll freeze the game.

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Stone Room: Umm... the comment that was originally attached to this code was rather cryptic, but if I understand it correctly, it's another way of saying that this is a two part code.  The Stone Room code will merely facilitate as where you arrive, and the second code (one of the enemy codes) determines what objects/exits are inside.  I'm not sure on this, though.  If you'd like to try and read it for yourself, here's JayTheHam's original comment:
"Firstly, these are file swapping codes, so you'll need to have both the code for the stage(in bold) you wish to go to and the code for the room you wish to go to active. When you load the stage the room who's code you have active will load instead of the default room(Room 0).

All rooms for this stage are the same but with different enemies."

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Beta Earth Temple Room With Miniblins: I have no idea what he's talking about with this comment, so I'll just post it here and let you guys take your own guesses as to what it means.
"Beta inside Fire Mountain - Hold Z."
Seems obvious, but what does that have to do with the code?

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