Twilight Princess has 4 Bottles for you to find. They can be used to hold various things. Unlike other Zelda games, they have a more unique design this time around.

Location: Ordon Shop (Ordon Village)
Requirements: Fishing Rod
Contains: 1/2 Milk

After you get the Fishing Rod, go to the dock and catch a fish. After that, you will have to catch another fish. The cat beside you will catch the second fish. Go back to the shop to get a reward for helping find Sera's cat.

Location: Faron Woods
Requirements: Cleared the Twilight
Contains: Lantern Oil

After clearing the Twilight and becoming human again, go see Coro and buy a oil-filled bottle for 100 Rupees.

Location: Fishing Hole
Requirements: Fishing Rod
Contains: Nothing

When you reach the Fishing Hole, don't go into the house just yet. Explore the area and you should find a little bridge with a little pond on the other side. Cast your rod into the pond. If you're lucky, you'll catch an Empty Bottle though you could always catch another fish or even a boot.

Location: Jovani's House (Hyrule Castle Town)
Requirements: 20 Poe Souls
Contains: Great Fairy's Tears

After collecting 20 souls of the Poes, head back to Jovani's House. After he is able to move again, he will reward you with a Bottle filled the tears of the Great Fairy.