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These are all the items you can use on the Select Item subscreen. Along with their pictures are descriptions on how to obtain them and how to use them.

Item Where to get it What it does
Bottled Items
Empty bottle

There are six bottles in all! One is given to you by Koume when she finds out that the skull kid got Kotake in the Woods of Mystery. Another is your prize for winning the big goron races. Romani gives you one for completing her archery test in under two minutes. The beavers of Waterfall Rapids will hand a bottle over to you when you beat both of them in an underwater race. Madame Aroma gives you one when you finally give her word of her son, Kafei. And finally, the last one is part of your spoils for going into the grave in Ikana graveyard on the night of the final day and defeating the Big Poe guarding it. If you see an item that is listed below, chances are you can bottle it! Stand close to it as you possibly can and take a swing at it.
Big Poe

Link must defeat this mighty adversary before he can bottle it. Once it falls, the big poe will leave its spirit behind. There are only two in the game (to my knowledge) so bottle 'em! It will be worth it! And here's why it's worth it. The man in the Curiosity shop will give you 200 rupees for one! Sweet deal.

These little guys are everywhere. They are pretty easy to spot. You can even hear them scurry around on the floor if you listen close enough for it. Since there are many places to find them, I'll just name a few easy places to retrieve them. Bugs can be found in Stock Pot Inn in the kitchen or in the farthest room on the second floor as well as several other places. Bugs aren't as useful as they were in Ocarina of Time. You'll need a few bugs to complete the first Skulltula house and there are a few mounds of soft soil that contain rupees in Termina Field and Romani Ranch. You can sell them for 20 rupees at the Curiosity shop, too.
Deku Princess

There is only one way to get this "treasure" of a item. After beating Odolwa in Woodfall temple, you'll be teleported to a room that holds the Deku princess. Cut her prison of vines away and bottle her up. Take her to her father and hilarity will ensue! Sadly, you can't sell her. Once you have completed the Deku princess quest, the butler will open his heart up to you and offer you a chance to play a game of tag.

Finding fairies is easy! Just break pots, cut grass and throw rocks. Basically, throw a tantrum! You'll find them! Also (though this is a little cheap...) if you find a room with a fairy hidden in it, exit then re-enter the room. Another fairy will have taken its place! Fairies are the most useful recovery items in the game. If you lose all your life energy, they will break out of the bottle they are in and restore some of your health, to a maximum of 10. If, for some reason, you don't want your fairy, sell it at the Curiosity shop for 20 rupees.

Search little streams and ponds for fish swimming around. Chances are there will be a few fish in the water. They prefer to swim in schools over swimming solo (though, there are some exceptions. ^_^) Fish are used very rarely. You need about five for one piece of heart in the Laboratory in Great Bay Coast and a few in the well. They sell for 20 rupees at the Curiosity shop if you are strapped for cash.
Gold dust

Become Speedy Gonzales and win the big goron races as goron Link. A strategy on how to be successful in doing so is on the Mini Games page. If you have the Razor sword on the second day, you can trade it in with the gold dust to forge the Gilded sword. Now... why is it that gold, one of the softest metals on Earth (I'll assume in Termina and Hyrule, too) can make a sword stronger... a gold alloy is not strong!
Magical Mushroom

Since these are magical mushrooms, they have to be invisible, right? Well, such is the case in Majora's Mask. Pull out your Mask of Scents (the only thing this mask is good for...) and look around the Woods of Mystery by Koume's potion hut. You'll see a purple cloud on the ground. Bottle the cloud and you'll get yourself some mushrooms. Koume needs these to make her awesome blue potion, but her old nose can't sniff them out as well as it used to. The poor old hag. Help her out by retrieving the mushrooms and she'll take them off your hands. Leave the hut then re-enter it and ask for a blue potion. She'll give it to you for free.

Three ways to get milk, but none are really worth it. Not when you've got fairies on your side, anyways. You can finish the archery test in less than two minutes and Malon will give you some. Playing Epona's song to a cow will help them lactate, giving you a bottle of milk. And finally, after winning against the Gorman brothers in the big race after you received Garo's mask, they will give you some watered down milk. Once you drink milk, you will regain five hearts of your life back. Though, it does have two servings, giving you a maximum of ten hearts, it doesn't revive you when you've died, making fairies a much better ally than milk.
Milk (Chateau Romani)

This elixir of magic is only available in one place, the East Clock Town Milk Bar. You can either buy it for 200 rupees (Ouch!) or you can get it as a reward for giving word of her son to Madame Aroma, but it is definitely worth it! Drink milk, love life! Is that how the saying went?? Chateau Romani is the pinnacle of all milks. Though only given in one serving, the milk restores some health and gives you unlimited magic for THREE DAYS! So drinking it on the first night will definitely save you the headache of searching for magic when you run out.
Potion (blue)

Only two places to pick up the best of the three potions, folks! One is in Koume's potion hut when you give her mushrooms and the other one is available by talking to the business scrub in Ikana Canyon (located by Sakon's Hideout.) Koume's potion is free and the business scrub's potion costs 100 rupees. This is the sweetest of potions! Regenerates full health and full magic! And it is in the prettiest colour of all three. ^_^
Potion (green)

Green potions are found anywhere you can buy potions so check out the West Clock Town General Store and Koume's potion hut. They'll get you what you seek! It will fill up your magic meter in a single gulp. Not bad for green goo.
Potion (red)

Ah, the life-giving potion. Before I learned that there were fairies in the Zelda games, I used to stock up on red potions. ^_^;; Silly me. Just like the green potion, the red potion is found in the General Store in West Clock Town and in Koume's potion hut. Also, if my memory serves me right, you can pick them up from the general stores in the Goron shrine and Zora hall. Feeling a bit injured? Chug this liquid down and feel your strength return. It will restore your health in one sip!
Sea horse

You can liberate the little guy from the fisherman on Great Bay Coast in the hut beside the skulltula house. You have to give the pervert of a fisherman a picture (a close-up picture o_O) of a Gerudo pirate. When he gets it, he lets out a lecherous "Oooooo." When you release your seahorse at Pinnacle Rock, he will show you the way through the misty waters. Once you get to the area with the deep pythons, you have a chance to the get a piece of heart if you eliminate all the deep pythons and save his other sea horse friend (or are they more than friends?)
Spring water

Anywhere in the swamp where Link can stand knee-deep in water, he can bottle it! Sometimes there are signs that tell him he can bottle the water places outside the swamp, too. Also, if you wait one minute with hot spring water, it will turn to regular spring water in an instant. Only one use for this item and that is to help your magic beans grow. Stand over your little bean sprout and pour some water on it. Your sprout will grow into a lovely hovering lilypad!
Spring water (hot)

There are three places to find some hot springs in Termina. Once you pull Darmani's tombstone from its place in the Mountain village, hot water will flood the room, creating one hot spring location. The other one in the Snowhead area is in a hole in the ground, covered with a chunk of ice by where Tingle floats around. The ice must be melted before you can gain entry. The last place is in the well in Ikana Canyon. Today's science lesson: Hot spring water melts ice! Astounding.
Zora egg

You can find Lulu's spawn in the Gerudo Fortress and Pinnacle Rock. See the Great Bay walkthrough for steps on how to obtain all seven eggs. Once all seven eggs are put together in the optimal environment of the Great Bay Laboratory, they will teach zora Link the New Wave Bossa Nova. They are child prodigies if they know how to teach guitar at one second old!
Event Items
Letter to Kafei

You'll obtain this important letter when you talk to Anju in the Stock Pot Inn's kitchen at 11:30pm. She'll tell you some plot stuff and ask you to deliver this letter for her. All you've got to do is drop this letter in a postbox in Clock Town. Any box will do as long as you deliver it before the postman comes and checks the box.
Moon's tear

Look through the telescope in the observatory in Clock Town and zoom in on the top of the clock tower. The Moon's tear will fall to the ground just outside the observatory. This jewel of all debris can be given to the business scrub in South Clock Town. He'll surrender his Land title deed, but you'll have to watch one of the more annoying cutscenes as he approaches and leaves the deku flower. Grrrr!!
Pendant of Memories

As a momento for your first visit (sort of...though it is really for Anju...) Kafei will give you the Pendant of Memories. See Bombers' Notebook for the steps on how to get to Kafei. Give this pendant to Anju before she decides to run away from Clock Town to join her family and friends at Romani Ranch on the final day.
Special Delivery

Note: You cannot get this item if you defeated Sakon in North Clock Town on the night of the first day because Kafei will still be in his house, having not seen Sakon himself! Anyways, when you meet with the man from the Curiosity shop in the afternoon of the final day, he will give you this special delivery! You have a choice for what you can do with this item (though, I would suggest doing both eventually!) You can give it to the fretting postman and he'll deliver the mail and flee from town OR you can deliver it yourself to Madame Aroma, who is in the Milk bar, drinking her miseries away.
Room key

Pick this handy, though not necessary item up by talking to Anju as any form of Link, but deku Link after her lunch break (make sure you don't talk to her before that time or she won't give it to you!) If you talk to her as deku Link, she'll treat you like a child. >_< The room key will open the middle room on the second floor and the front door of the inn at anytime of the night. No more sneaking in from the roof's door for you! Also, there are 100 rupees in the chest in your room, so pillage!
Title deed (mountain)

Outside the Goron Shrine is a business scrub who wants something new and deku Link has what he's looking for. If you have the swamp title deed, talk to the scrub as deku Link, though you may want to talk to him as goron Link first to get the Biggest Bomb bag (see Equipment.) If you give him the swamp title deed, he'll move to the swamp and give you this deed! Hop in the deku flower and face the snowy wall. Launch up and you'll see a piece of heart on the ledge. Glide to it and you'll be one piece of heart richer! Also, this deed is used to get the ocean title deed.
Title deed (ocean)

There is a business scrub living inside Zora Hall who wishes he were outside in the crisp, clean air of the mountains so grant him his wish! Talk to him in the leftmost room in Zora Hall as goron Link so you can give him the mountain title deed! In exchange for the change in scenery he so desperately craves, he'll give you the ocean title deed! Into the deku flower you've just obtained and launch yourself onto the ledge with the piece of heart on it. If you so wish, pick it up. ^_^
Title deed (swamp)

Poison water. Living on a deck. No business in sight. Who would want to move from this awesome site?? The spoiled business scrub in the southern swamp, that's who! Talk to him as human Link and he'll ask you for some land in Clock Town. Give him the town land title deed if you have it and he'll be so excited, he'll move right away, leaving you with the swamp title deed. On top of the tourist information hut is another piece of heart. Use the deku flower to get onto the roof and add it to your collection.
Title deed (town land)

Trouble with the wife is why this business scrub hasn't gone home yet. He needs to find the prettiest jewel in all of Clock Town before he can even think of facing off against the wife. Luckily, one of these jewels falls from the sky every cycle of three days, eh?? Pick up the Moon's tear and give it to him. He'll trade his town land title deed for it. Glide over to the clock tower platform with the piece of heart on it when the new deku flower you just received.
Equipable Items
Arrows (fire)

After defeating the first wizrobe in Snowhead temple, you will be rewarded with ice's bane. These can be used to melt ice and light braziers. Equip them with the hero's bow and everything will get a little hotter. (Ooooo, bad joke.)
Arrows (ice)

Your prize for defeating Wart is the ice arrows. Ice arrows are much more useful in Majora's Mask than in Ocarina of Time as they are actually required. Freeze certain enemies into climbable blocks, create mini ice platforms in the water and freeze waterfalls. Cool. (Ooooo, another bad one! >_< )
Arrows (light)

Take out the Garo master and he will give you some advice and the light arrows. Activating light switches and weakening darkness enemies is what the light arrows do best. These ain't no shots in the dark! (Ooooo, third times the charm. No? No...)

Buy a bomb bag in West Clock Town, either at the Bomb shop or the Curiosity shop (though the Bomb shop is cheaper! ^_^) You can pull bombs out and blow crap up! Stay still and put the bomb at your feet or run with it and throw them.

You can purchase these at your local Bomb shop or find them in chests in holes in the ground. Only used twice in optional parts in the game, they are mobile bombs. Take them out and place them at your feet. They'll take off and blow up after going a certain distance or hitting something flammable.
Deku nuts

A deku baba's dead carcass may leave behind a deku nut if it isn't killed while sticking straight up. Also, a mad scrub may leave one once you have wasted it away to nothing! Throw them at certain enemies and they will be stunned for a few seconds. Not terribly useful... I don't think I've ever used them in Majora's Mask, actually...
Deku stick

A stunned deku baba with give you a deku stick. You can find them in pots, too if you are in a room that requires at least one stick. Bring out the stick and you've got yourself a really long weapon. Problem is they break on contact with anything so be careful. Also, you can set the top of the stick on fire and carry it around like a torch to light braziers. Make sure you put it away before the fire burns the whole stick, though or you'll have to bring out a new one.
Great Fairy's sword

Given to you by the Great Fairy of Kindness, this sword is colourful and powerful. Collect all fifteen fairies in the Stone Tower Temple and visit this Great Fairy. One thing I don't understand is why the Great Fairy of Power doesn't give you this sword... This is a C button sword. I've never used it, but it does have longer reach and is possibly better at giving damage. I will test this theory soon.

Metal Gear Solid your way through the Pirate's Fortress and you'll be rewarded with the legendary hookshot! The hookshot has got a bit of a makeover, but it does the same thing. Look for wooden posts, boards and trees that the hookshot will stick into then hold on for a sweet ride. You'll be pulled to wherever the hookshot got stuck. Normally, the hookshot could pull things to you, but the only things that seem to do that in this game are enemies. Any enemies the hookshot will stick in will also be stunned, giving you a few free smacks.
Lens of truth

Take a leap of faith... then several more. Cross the abyss in the Goron city where Kaepora Gaebora is sitting and sheds some wisdom on you... and his feathers on the invisible platforms. The cave at the other end of the abyss holds the lens of truth. See what is unseen with the lens of truth. Anything invisible becomes un-invisible...I mean visible. It does take magic to use, so make sure your magic meter has a little juice left in it before whipping this baby out.
Magic beans

There are two places (techinically three) to pick up the magical fruit. In the hole in the right garden, there is the bean man from Ocarina of Time and he's back at it... selling beans... Also, talk to the business scrub who originally lives in Woodfall as deku Link or when he moves to Clock Town, as anyone and he'll sell you the beans you crave! Plant them in soft soil and pour some spring water on them. Watch them grow! Like Chia Pets!
Ocarina of Time

Ah, music to my ears. You have to get this back from the skull kid during your first three day cycle in Clock Town. Hit the skull kid with a snot bubble and retrieve what he stole from you! You can play magic songs with the ocarina! Each C button and the A button are notes so play to your heart's content. Also, if you want to have a little fun, wiggle the joystick around while playing to change the pitch of the notes you've played. The R button also changes the pitch. You can play lots of different songs. I learned how to play the Super Mario overworld theme! ^_^
Pictograph box

Koume is a much nicer person than she was in Ocarina of Time. Before she was trying to kill you with her sister, Kotake as Twinrova. Now she gives you a pictograph box for saving her in the Woods of Mystery. ^_^ Take pictures! Though, I think you only need two pictures in the whole game (and one is optional...) you can only hold one picture in your box so hopefully, it is the one you need!
Powder keg

Take Biggoron's grueling training course and pass to receive the powder kegs. Follow the end of the Snowhead temple walkthrough for tips on how to pass the training session with flying colours. Pick these Tnt drums from Biggoron for 100 rupees or from the goron in the Bomb shop for 50 rupees... which one will you choose to shop with??

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