Bomb Bag UpgradesThere are 3 bomb bags to obtain and 1 capacity upgrade that affects all 3 bags.
Bomb Bag 1 - Purchace from Barnes Bomb Shop in Kakariko after 2nd temple.
Bomb Bag 2 - Free the goron from the giant lava rock located underwater in zoras domain.
Bomb Bag 3 - Destroy the rock barriers for the River Canoe mini-game owner.
Bomb Bag Capacity Upgrade - Score 25 points or more on the River Canoe Mini-Game.
Bottle: Fishing HoleGo to the fishing hole, and find the sign that says: No Littering! You can get a bottle if you fish on the left side of the bridge that is near that sign. Its darker water than normal.
FairiesAfter locating the Gerudo Mesa and Cave of Ordeals in the Gerudo desert, you are able to unlock fairies and later Great Fairies at each spring around Hyrule. Smaller fairies can be bottled, restore 8 hearts when used, or when you run out of hearts. Great Fairies will give you a bottle full of Great Fairy Tears, which heal you full and temporarily boost your attack, provided you have an empty bottle and no Tears in your inventory already.
Both have an infinite supply once unlocked.
Fairies in the Eldin Spring - Complete 30 rooms in the Cave of Ordeals
Fairies in the Faron Spring - Complete 20 rooms in the Cave of Ordeals
Fairies in the Lanayru Spring - Complete 40 rooms in the Cave of Ordeals
Fairies in the Ordon Spring - Complete 10 rooms in the Cave of Ordeals
Great Fairies in all springs - Complete 50 rooms in the Cave of Ordeals
Frog Fishing LureTo unlock the Frog Fishing Lure for the Fishing Hole, you must beat all eight levels of Roal Goal, a game found in the owner's establishment. To play it, simply look at it in first person using the C button.
The game requires 5 rupees a play and you win 10 rupees for each round, and the frog lure for the eighth. (If you run short before you manage to get the lure, mowing the tall grass just outside (still in the fishing hole area) offers around 60 rupees.)
Lure description: The must-have lure for bass.
Malo Mart-Castle Branch and Magic ArmorAfter donating 1000 rupees and completing the hot springwater sidequest, donate 2000 more rupees to Malo Mart. A new Malo Mart will open in Castle Town and magic armor will be available for purchase there. The amount owed can be reduced (see Secrets section below).
Poe RewardsYou can unlock certain rewards for returning Poes back to Jovani.
200 Rupees (talk to him again for another 200) - Bring back 60 Poe Souls to Jovani.
Bottle W/ Fairy Tears - Bring back 20 Poe Souls to Jovani.
Quiver UpgradesTo upgrade you arrow capacity, you need to play the "STAR" game located in the large tent in Southeast Hyrule Castle Town.
Big Quiver (60 Arrows) - Beat "STAR" game lvl. 1. (Clawshot Required)
Giant Quiver (100 Arrows) - Beat "STAR" game lvl. 2 .(Double Clawshot Required)
Sinker LureTo obtain the Sinker Lure you must first catch a Hylain Pike, Hyrule Bass, and a Ordon Catfish in the fishing hole area with the lure rod. After you have caught one of each you go to the south east corner of the water closest to the house and take out your Fishing Rod(bobber) with the coral earring hook. After that you will catch the Sinker Lure. Make sure Hena doesn't see you use it or she will take it away.
Unlock Special-Edition RollgoalIf you visit the Fishing Hole in Upper Zora's River, there's a mini game Hena will let you play for 5 Rupees called Rollgoal. If you make it past 1-8, you'll be rewarded with the Frog Lure. However, if you keep going and beat the entire thing, up to and including 8-8, you'll be able to play the special-edition version of Rollgoal. You can choose any level, the cost is free, the time limit is raised to 4:00:00, and you cannot win any Rupees. Also, as an added bonus, once you beat 8-8, Hena will fill your wallet completely!
Wallet UpgradesTo upgrade your wallet size to carry more rupees, you need to catch Golden bugs for Agatha in Hyrule Castle Town.
Big Wallet - Give Agatha 1 Golden Bug
Giant Wallet - Give Agatha all 24 Golden Bugs
Easter EggsControl a Cucco!Unlike other Zelda games (where you got attacked if you hit the Cuccos), in Twilight Princess if you hit a Cucco about 8 times, you'll be able to control it for a short period of time.
GlitchesInfinite Bomb GlitchFirst, as a wolf, play PLumm's minigame with the fruit and crash. Then, turn back into a human and turn to the water behind you. While swimming in it, equip the hookshot, and while it is held out, strafe tothe side and through the wall. If it works, you'll be swimming through the wall. Keep swimming until you flall and die. Now, as you wake up, Plumm will come back and ask to to play again. Say yes. Then crash at the beginning again. You should wake back up in the beyond-the-wall area from before, but you can stand. Turn into a wolf and jump into the waterfall. Then, you'll wake up in front of Iza's assistant. Say yes, and you'll go to her cabin. The boat will take off without you, and you'll be a wolf. So now, warp anywhere you want, and you'll have infinite bombs.
Note: This ends when you turn off the game, sadly
Magnetic Ceiling GlitchThis can be done wherever there is a magnetic ceiling, such as the first one encountered in Death Mountain Mines.
First equip the boots to the D-pad but don’t put them on. Go under the magnetic field and equip the boots. In mid flight up to the ceiling press the - button and put an item where the iron boots were on the D-pad, and make sure the Iron boots are not anywhere on the D-Pad. Unpause the game and finish flying onto the ceiling. You should be on the ceiling with the Iron boots off and you will stay there and be able to walk faster.
To get down walk off the magnetic part of the ceiling or equip and unepuip the Iron Boots.
SecretsDaytime WheneverYou need to be able to get to the City in the Sky. At whenever time you go there, when you come back, it will always be daytime.
Distract the final Boss's final form with the fishing poleThe true final boss of this game can be distraced by the fishing rod. Just cast it out while Z-Targeting him and his head will turn to look at the lure. Quickly put away the fishing pole and get in a few quick attacks.
Donation ReductionDonate 1000 rupees to Goron inside the Malo Mart in Kakariko Village (you must progress past the third dungeon beforehand). Talk to the old Goron outside the shop and complete the quest he offers. Once completed, the second donation amount will be reduced from 2000 to 200 rupees.
Easily Recover Heart PiecesTo easily find the locations of all Heart Pieces, go to Fanadi's Palace in Hyrule Castle Town and pay her 10 Rupees for a Love fortune. You will then see an area in the game that will contain a Heart Piece around it, obtainable in some fashion. You can keep paying her to show you other locations, but she will sometimes repeat the same location a few times over.
Worms for FishingIf you go into the fishing hole behind the sign at the very entrance there will 3 little mounds of dirt.
Turn into the wolf and dig these up, earth worms will appear, scoop them up in an empty bottle and use them as bait for your fishing hook to make fishing extra easy!
The big concept twist that 
