Favorite Tool: Probably the Hookshot, especially the double clawshot from TP and SS. My second choice would either be the Pegasus Boots or the Roc Feather.

Favorite Game specific Tool: Probably the masks from Majora's Mask. bit specifically either the Bunny Ears that doubled your speed, or the Goron Mask.

Favorite Dungeon: Oof, tough one. Either the Thieves Hideout from LttP, it's Lorule counterpart in ALBW, or Death Mountain from TP.

Least Favorite: I feel the easy low hanging fruit here would be to list off the dungeons from Zelda 2, but that feels like a cop out. I'm going to say either Level 6 from Zelda 1 where Wizzrobes are first introduced, the Fire Temple from OoT cause I find it annoying to track down all the Gorons, The Great Bay Dungeon from MM cause it's even more annoying than OoT's Water Temple, or the Ocean King Temple from Phantom Hourglass for being kind of repetitive and slowing down the game.

Update Time:
I've finished the Dark Palace and Skull Woods Dungeon, forgot I had to figure out a password to get into the Thieves Dungeon but I was oddly able to figure it out without much effort when I actually tried. I was able to gain two pieces of Master Ore, allowing the Hyrule Blacksmith to upgrade the Master Sword to its tempered form. I'm still a glass cannon, but the cannon part is being heavily emphasized. I was also finally able to buy all of the available weapons. I'm still missing the Sand Wand since one of the Sages has it and I can't quite figure out which temple he's specifically at. Knowing my luck, he's at he Water themed dungeon, which requires I get the Titan Mitts first to reach since it retained the annoying "do something in the Light World to affect the Dark World" which technically shouldn't really work in this game when I think about it. What really irks me is that the Swamp dungeon has the damn Blue Tunic in this game, and I need the Sand Wand to get there.

I do feel I need to start training in my alien squid babies for Item upgrades, but I need to check what I've accomplished so far so I don't accidentally lock myself out of the optional boss. Thankfully, I've already accomplished one of the tougher challenges in beating an opponent with the Lantern. That one is a bitch. I've collected over sixty of the alien squid babies, so I really don't have much left to go.

More Questions:

Favorite Dungeon Boss (No Final bosses)?
Least Favorite Dungeon Boss?
Favorite Minigame?
Least Favorite?