I'd say of the 3d console games it's Wind Waker and Majora's Mask. The Nintendo Gallery alone is harder than 100% on OOT, not to mention the freakish amount of other things to collect. Plus if you're doing "everything" you have to do the puzzles on the wall in the cabana. For Majora's Mask the stray fairy collection gets absolutely ridiculous in the Stone Tower Temple, and I can't imagine the typical Zelda player getting all of them. So Wind Waker > Majora's Mask > Twilight Princess because the Poe and Bug collection is much harder than Golden Skulltula collection plus TP has 9 more pieces of heart and a cave of ordeals. OOT and SS are both kind of really easy. OOT the subscreen will make it easy to find all the skulltulas since the game tells you if you've found them all in an area, but heart pieces are still tricky in some cases. In SS there's very little that doesn't have significant in game hints so anyone can 100% it. Even getting the Hylian Shield on Hero Mode is doable for anyone since the game lets you use potion effects if you drink them before starting the boss rush (guardian potion plus).
Across all games the Oracles and Minish Cap are also difficult. Also just throwing this out there that the original Zelda is pretty absurd without a guide. Don't forget that there's a second quest either and a couple of heart piece locations are absolutely crazy in that quest not to mention that most people will never find level 8 anyway. Zelda II, ALTTP, and LA are actually not that bad though. Most people don't finish Zelda II though so I guess that technically makes it hard to 100% even though item collection is fairly easy.
Hmmmm..... I wouldn't agree Wind Waker is the hardest. It has several in-game guides in the form of the charts (i.e. Heart Piece Location Guide, Crow's Nest Locator, etc). I would think Majora's Mask is hardest because of its tons of Heart Pieces and Masks to collect.
There's no guide for the Nintendo Gallery and you can make it much harder by doing it on the first quest which makes things missable. Majora's Mask actually has several guides as well but they aren't super obvious like in other Zelda games. The Stray Fairy Mask let's you know when a stray fairy is in the room, there are Gossip Stones on the moon which tell you where every mask is so if you are missing a few you'll find them, and the Bombers' Notebook fills in when you have to do something related to the person after they get an entry in the book.