Kakariko Cucco Lady — Anju's Cuccos have scattered around Kakariko Village. Catch all seven and drop them in her pen (check the scaffolding, behind houses and near the windmill). She rewards you with an Empty Bottle.
Lon Lon Ranch Super Cucco game — Talk to Talon in the ranch house and pay for his game. He tosses three Super Cuccos among the ordinary ones; find all three before the timer runs out. He gives you Lon Lon Milk, and the bottle is yours to keep once you drink it.
Ruto's Letter (Lake Hylia) — A bottle holding Princess Ruto's letter sits on the lake bed where you surface from the Zora's Domain passage. Dive down for it, show the letter to King Zora, and the emptied bottle stays in your inventory. This one is required for the main quest.
Poe Collector (10 Big Poes) — Ten Big Poes haunt Hyrule Field. Each bottled spirit is worth 50 Rupees and 100 points at the Poe Collector's shop; after you turn in all ten (1000 points) he hands over an Empty Bottle. You can hold at most three spirits at a time, so plan several trips.