A list of the locations where you can find empty bottles in The Legend of Zelda: Skyward Sword.
Empty Bottle #1 - Luv in the Skyloft Bazaar
After you unlock the Green Column in the sky, you can go to the Bazaar in Skyloft and talk to Luv at the Potion Shop to get a free Empty Bottle.
Empty Bottle #2 - Treasure Chest in Sealed Temple
After you first descend to the surface, you can find a treasure chest in the Sealed Temple near the Old One. The chest contains a bottle that has a Revitalizing Potion inside. After you use the potion, you keep the empty bottle.
Empty Bottle #3 - Help Orielle
After you unlock the red column of light, go south from the Goddess Statue and talk to Wryna, and agree to help find Kukiel. After you find Kukiel, you can talk to Parrow in the plaza during the day and agree to help find his sister. Fly toward the colorful island in the southwest of the sky, but before you get there, look for the small island with the injured Loftwing on it. Talk to Orielle, who is next to the Loftwing, then fly back to Parrow to get the mushroom spores. Take them back to Orielle to get some Gratitude Crystals, then go back to Skyloft and talk to Parrow to get more Gratitude Crystals. You can keep the empty bottle, as well.
Empty Bottle #4 - Fire Sanctuary
There is a blue chest in the eastern side of 1F of the Fire Sanctuary that contains an Empty Bottle.
Empty Bottle #5 - Goddess Cube Chest
After Levias asks you to learn the three dragons' songs, there will be a volcanic eruption the next time you go to Eldin Volcano. After you retrieve your sword, you can go east into the lava room and use a Skyward Strike on the Goddess Cube there. It unlocks a chest in the thunderhead, on a small round island between the two large islands in the north and south. Land on the southern end of the island, where there is a digging spot in the ground. Dig into it and kill the Moldorm, then go to one of the beams of light in the corner. If you emerge at the correct one, you can climb up the vines to reach the chest, which contains an Empty Bottle. (The wrong one just leads to a different chest.)