Deku stick upgrade - there is a glitch that prevents you from getting one of the upgrades (standing on the Forest Stage wearing a skull mask) if you have already pulled the Master Sword.
Bottles -
1. Gathering Cuccos in Kakariko village and putting them in the pen (Child)
2. That Cucco finding game at Lon-Lon Ranch (Child)
3. Story related (child)
4. Gathering 10 big poes (Adult)
EDIT: Ninja'd >_<
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One less bracket.
http://myanimelist.net/profile/tyder21