Organization of Upgrades
There are lots of different items and they can be categorized in many different ways. Suggest and weigh methods here.
My suggestion would be to follow the game menus. One page for all the 'dungeon' items that show up on the 'B' menu, one page for all the shields and bottles, one page for all the collectibles, one page for equipment (e.g. tunic), and one page for other items like quest items (e.g. keys, trading sequence, "Bird Statue"). Deviating slightly, it might make more sense to put the shields on the Items or Equipment page, leaving the bottles and bottled items separate like they are in the OoT guide. Essentially, I think grouping similar items, cutting down on the total number of pages, would make it easier to navigate and harder to pick the 'wrong page.'--Locke 21:46, 20 September 2011 (CDT)
Merging Equipment/Items with Upgrades
Looking at the Upgrades page and the Equipment page from Ocarina of Time, I find that the two are a bit redundant. Why not just combine the two? I set up an example with the shields on my userpage User:Locke. Otherwise, the items/equipment page would briefly mention the upgrades and the upgrade page would add very little information (rupees, ingredients, new abilities).--Locke 21:46, 20 September 2011 (CDT)
Insects/Treasures/??? on one page or separate pages?
Looking again at the Ocarina of Time guide, I think the Items page would be a good way of organizing the collectibles, all on one "Collectibles" page.--Locke 21:46, 20 September 2011 (CDT)