Kokiri Tunic - In my opinion it makes Link look the most heroic. I mean, knights are supposed to be heroic--amongst other things--and since this tunic originally had such significance it can only seem fitting to Link's character. Especially when considering he is the Hero of Time.
Hylian Shield - I prefer this over the Wooden Shield because it's unbreakable, doesn't burn, and looks a whole lot better designed. I don't like that Young Link can only wield it on his back, as even that leaves him open to harm in some instances.
Kokiri Boots - Simply because they don't impede your movement and have no gimmicks attached.
Master Sword - Allows for more challenge because it doesn't do near the amount of damage given by Biggoron's Sword, but is still able to combat any enemy quickly. Also it doesn't break like that irksome Giant's Knife did, and ultimately is the only tool used to kill Ganondorf.