Finished completing my second time through last night, and I was working on a good path for 100%-ish speed run.
When I am in an area already for a dungeon, I try to clear the area out of maiamais, pieces of heart, mini-dungeons, etc, too.
Eastern Palace
(Get Flippers, Pegasus Boots, Power Glove)
House of Gales
Tower of Hera [debating whether it is better to do this before Gales, since I would already have been on the north side of Hyrule to gather items]
Hyrule Castle
Thieves' Hideout (for the Master Ore and getting the Sand Rod for the Desert Palace)
Desert Palace (to get Titan's Mitt; now I am able to access all hidden items)
(Get Master Ore by the Graveyard, clear out that small area of Lorule, can now get upgraded Sword.)
Swamp Palace (On Hero Mode, I might do this before Thieves' Hideout to have the Blue Mail earlier)
(Finish clearing out the large southwest area of Lorule including getting lots of Rupees at the Rupee Rush -- see my post about that, buy most items from Ravio)
Skull Woods (for the Master Ore and then clear out that area of Lorule)
(Head up to the Treacherous Tower and get the upgraded Lamp for going to the Dark Palace)
Dark Palace (final piece of Master Ore and then clear out that area)
(Get final upgrade to Sword, Treacherous Tower again (with stronger sword) for upgraded Net)
[I am not sure how helpful the upgraded lamp is for the Dark Palace, something I read somewhere suggested it. If it is not, my path would instead be: Dark Palace, Skull Woods, Sword upgrade, all of Treacherous Tower]
Turtle Rock (I do not use the shield as much so I am okay to wait on upgrading it, clear out the southeast area of Lorule)
Ice Palace (and clear out Death Mountain)
Lorule Castle
