
There are four Empty Bottles in Twilight Princess HD, in the same places as in the original. Bottles hold Red, Green and Blue Potions, Lantern Oil, milk, soup, fairies, bugs and more, so they're well worth tracking down. Two of them come with something already inside.
Sera's cat hasn't come home. Catch a fish with your Fishing Rod (in HD the first fish is enough) and the cat will grab it and head back to Sera's Sundries. Follow it to the shop, and Sera thanks you with a bottle half full of Ordon Goat Milk.
Cost: 100 Rupees.
After the twilight has been cleared from Faron Woods, Coro, who lives in the house by the entrance to the woods, offers to sell you a bottle of Lantern Oil for 100 Rupees. You keep the bottle once the oil is used up.
Once Lake Hylia has been restored and you can reach the Fishing Hole, look for the small pond by the "no littering" sign near the bridge. Cast your regular Fishing Rod (not one of Hena's lure rods) into the pond and you'll reel in an Empty Bottle.
Jovani has been cursed and turned to gold. Collect Poe Souls as Wolf Link and bring them to his house in Castle Town. Once you've collected 20, he gives you a bottle filled with Great Fairy's Tears. He also gives you the Ghost Lantern, which glows whenever a Poe is nearby.