You can get a total of four empty bottles in Wind Waker. Here is a list of each one, with instructions on how to get them.
Empty Bottle #1
You will receive this bottle after helping Medli reach Dragon Roost Cavern.
Empty Bottle #2
Go to Windfall Island at night and walk to the building with the big red door. Talk to Mila, the girl dressed in rags. Walk up the stairs until she starts running. Now you will have to be careful. Follow her but keep your distance to prevent her from seeing you. If she runs away, go into a building and go back out, then talk to Mila near the red door again. Just stay as far away as you can without losing sight of her.
She stops by the potion shop, then she goes under the arch toward the pier, stops a while, then goes up the hill to her right, stops, goes up the wooden ramp and through the arch there, stops in the courtyard (the best place for you to hide while she's standing there is to stay near the edge of the wooden ramp, and turn so you can see through the arch for when she starts running again), then she goes down the path next to the staircase, stops at the base of the hill, and then she runs into Zunari's shop and fiddles with the safe. Run up to her while she has the rupee thought bubble above her head, and talk to her. Choose the top option every time, and you get an empty bottle.
Empty Bottle #3
Sail one square north of the Forest Haven to reach Bomb Island. Go into the submarine in the center of the Bomb Island map square. Kill all of the bokoblins inside to receive this empty bottle.
Empty Bottle #4
Buy an empty bottle from Beedle's Rock Spire Isle shop for 500 rupees.