The first bottle that you can obtain is at Lon Lon Ranch after Talon and Malon have returned to the ranch following their visit to Hyrule Castle. Enter the house on the left side to find Talon sleeping near the table surrounded by Cuccos.
Talk to Talon to initiate a mini-game where you have to locate his three Super Cuccos amongst all of the regular Cuccos despite them all looking exactly the same.
The easiest way to complete this mini-game is to prepare by picking up all of the Cuccos and throwing them in behind the table where Talon is sleeping. The reward for successfully finding all three of Talon’s Super Cuccos is a Bottle of Lon Lon Milk. The Milk will heal you when you drink it, but the true reward is the Bottle, which has a ton uses throughout the game.
The second Bottle is obtained as a reward in Kakariko Village. Find a woman standing near an empty pen and speak to her to find out that all of her Cuccos have flown away. She will ask you to bring them back to her and throw them into the pen for her.
The first Cucco is located right near the pen – run over and pick it up but don’t throw it into the Cucco pen just yet. Climb the stairs to the building just south of the Cucco pen (the one that is under construction).
You should see a Cucco near the entrance to the House of Skulltula. The only way to reach this Cucco is to use another Cucco to fly over. Glide down to the ledge and then throw both Cuccos down.
Grab one of the Cuccos again and take the stairs to the east of where the woman is standing up towards the windmill. Use this Cucco to glide from the top of this walkway down towards the balcony of the red house as shown in the screenshot below.
Turn around and throw the Cucco off the balcony down below and then run down to the lower area, grab the other Cucco and take it up to the balcony to throw it off too.
There is one last Cucco in this area though which can be found by climbing the ladder on the east wall. The Cucco is wandering around on the grass next to the Windmill.
There is another Cucco up near the entrance to Kakariko Village where the guard was standing. You can also find another one in the crate near one of the houses. Just roll into it to release the Cucco.
The last Cucco is located up near the entrance to the Death Mountain Trail. That should be all of them. Speak to the woman again to receive your reward – a shiny new Bottle.
The third Bottle is obtained naturally during a regular playthrough of the game. You obtain it in Lake Hylia when Link searches for the note from Princess Ruto. Check out the Lake Hylia walkthrough page for more information.
This Bottle can only be obtained after Link has completed the Forest Temple and obtained the 
Fairy Bow.
The Ghost Shop can be found in the guard tower between Hyrule Market and Hyrule Field. Enter the guard tower to now find a weird looking ghost creature who has set up shop here.
Speak to the Ghost a second time and he will ask if you have any Poes. He will provide you with a card where you can obtain points for obtaining Poes. Each Big Poe counts for 100 points and you need 1000 in order to receive the reward (the empty Bottle).
Start things off by emptying each of your other three bottles as you will need them all in order to hold the Big Poes. Hunting Poes is fairly straight forward – they can all be found on the world map. You have to defeat them using your Fairy Bow and then capture them.
Hit them with two arrows quickly in succession while mounted on Epona and then touch them to store them in a bottle. All you have to do to capture them is touch them while Link is on foot and he will automatically put the Big Poe in an empty Bottle (assuming you have space).
Note: If you find yourself running out of arrows for the Fairy Bow just return to the entrance to Zora’s River and destroy the plants right up front. Leave the area and return and they will be back. Repeat this until a few arrows appear.
Some tips for defeating the Big Poes:
1) The Big Poes appear when you stand in the correct area of the map, but they always appear directly in front of Epona, no matter which direction the horse is facing. As a result, this can cause the Big Poes to fly through walls. Keep this in mind and try to aim Epona in a direction where you can get clear shots at the Big Poe once it appears.
2) You do not have to be moving for the Big Poe to appear, but once it gets far enough away it will disappear. If you shoot your arrows very fast in succession you can defeat a Big Poe without moving.
The first Big Poe is located right out front of Hyrule Castle. Call Epona over, jump on, and ride directly south fairly quickly and a Big Poe will appear. Run past the sign to ensure that the Poe appears.
The second Big Poe is located just outside of Lon Lon Ranch. Travel between the tree and the edge of the ranch headed eastbound to make it appear.
The third Big Poe is located near the river to the west of Hyrule Castle. Run east and west along the river to make the Poe appear.
The fourth Big Poe is located along the trail heading north and south near the entrance to Gerudo Valley.
The fifth Big Poe is located near the entrance to Kakariko Village. On the west side of the river is a large plateau that juts out over the river. Back Epona up to the edge of the plateau and face southward.
You do not need to be moving in order to make the Big Poe appear. Just wait there and it will keep appearing. Aiming and hitting this one before it disappears is very difficult.
The sixth Big Poe is located on the pathway between Kakariko Village and Lon Lon Ranch. Use the mini-map to locate the point where three paths connect. There is a large boulder near the fork – approach it to make the Big Poe appear.
The seventh Big Poe is located just south of the last one. There is a large pine tree with a group of shrubs beside it. Run through the shrubs to make the Big Poe appear.
The eighth Big Poe is located just south of the previous one amidst the trees. You can make it appear by riding fairly close to the large boulder, somewhat to the southeast.
The ninth Big Poe can be found near the stone wall to the east of Lon Lon Ranch. You can make it appear by riding very close to the wall (on either the west or east side of the wall, which ever you find easiest).
The tenth Big Poe is also located near Gerudo Valley. There is a tree just north of the pathway running north and south. Run past the lone tree to make the last Big Poe appear.
Return all 10 Big Poes to be certified a genuine “Ghost Hunter” and to receive the Empty Bottle as a reward. You now have all 4 Bottles.
You now have all four Bottles which can be obtained in the game.
