V2 of the ruling is up, fixing the i.e./e.g. thing, and adding a few more technicalities (such as bottle duping over an empty item slot). The ruling on 1b/2d will have to be discussed further before a change is made.
1. Any item that appears in your Item Subscreen counts. (e.g. bottle, megaton hammer, light arrows)
1a. All items in the same slot (even if they are at different times) in your item subscreen count. (e.g. if you get Egg, then Cucco, it counts as two items; the same is true of hookshot and longshot, etc)
1b. Previous items are not assumed in any item. (e.g. if you get Zelda's Letter, you do not automatically get Egg and Cucco)
1c. Transforming an item into a bottle does NOT count as an additional item (e.g. turning Deku Sticks into a bottle with bottle duplication)
1d. Using bottle duplication to get a bottle on an empty slot does NOT count as an additional item
2. An item that appear on your Equipment Subscreen counts. (e.g. quiver, master sword, iron boots)
2a. Kokiri Boots and Tunic do not count, since they are obtained at the start and are never "collected".
2b. All items in the same slot (even if they are at different times) in your item subscreen count. (e.g. if you get Bomb Bag, then Big Bomb Bag, it counts as two items)
2c. As a clarification for 2b, Giant's Knife and Broken's Giant Knife are two different items.
2d. Previous items are not assumed in any item. (e.g. if you get Golden Scale, you do not automatically get Silver Scale)
3. Every Heart Container or Heart Piece counts as one item.
3a. The first three hearts you get do not count, since they are obtained at the start and are never "collected".
4. Any Great Fairy Gift counts as one item. (e.g. Magic, Double Magic, Double Defense)
5. Any wallet upgrade counts as one item. (e.g. Giant's Wallet)
5a. The starting wallet does not count, since it is obtained at the start and is never "collected".
6. Any song learned counts as one item. (e.g. Song of Time, Zelda's Lullaby)
6a. Scarecrow's Song counts as one item.
7. Any Medallion or Spiritual Stone counts as one item. (e.g. Light Medallion, Kokiri Emerald)
8. Gerudo License and Stone of Agony count as one item each.
9. Epona and the cow in Link's house count as one item each.
10. Each Golden Skulltula token collected counts as one item. Any reward from the Gold Skulltula House counts based on the other rules. (e.g. Adult's Wallet counts, silver rupee does not)
11. Ammunition does not count as an item. (e.g. arrows, nuts)
11a. To clarify, ammunition-in-themsleves items, such as Deku Nuts and Deku Sticks, do count as one item when they are first picked up.
11b. Anything caught in a bottle is considered "ammunition" and is not counted as an item. (e.g. bugs, fish, poe)
11c. All types of rupees are classified as ammunition
12. Dungeon items do not count as an item. (e.g. Small Keys, Boss Keys, Dungeon Maps, Compasses)
13. Any item obtained in the fishing pond does not count as an item. (e.g. fishing pole, fisherman's hat, 6 lb fish, sinking lure)
13a. If the item obtained would count under a previous rule, it is still counted. (e.g. Heart Piece, Golden Scale)
14. If an item is lost and then regained, it is not counted again. (e.g. burning a Deku Shield and buying another, getting a hylian shield back from a Like Like)
15. If an item that would count under a previous rule appears on B, it counts as obtaining that item.
16. Deleting an item through RBA or any other means does not remove the item from your count.