My personal favorite game of all time is Eternal Darkness for the gamecube. Amazing storyline and atmosphere and just completely trippy experience, nothing else like it.

Zelda? My favorite is Ocarina of Time: Master Quest followed by Majora's Mask. My least favorite would probably be Adventures of Link. Wind Waker was just way way too easy and short. Twilight Princess is good just too easy as well. Nintendo needs to start introducing difficulty settings for their games.