1. Ocarina of Time-A holy construct almost, Ocarina of Time is pure videogame bliss and perfection. The dungeons, character, music and sidequests are seamlessly blended together in order to create a consummate whole. The ocarina is the best instrument in franchise history. Period. Phantom Ganon and Bongo Bongo are some of the best boss battles in franchise history. Areas are varied spanning from the Kokiri Forest to Gerudo Desert. Characters are very well developed from the most important like Shiek and Malon to lesser ones including the carpenters. Kakariko Village, Goron Village, and the Temple of Time are namesakes I shall never forget.
2. The Wind Waker-The Wind Waker may seem like a kiddie child's tale at the beginning but its's so much more. Gamecube's first and only exclusive Zelda game is a story of love and hate, friendship and jealousy, vice and virtue. Character development is at its absolute best here. Seeing Aryll kidnapped and being reunited with here for only a moment is truly touching but it's the powerful character of Ganondorf who seals the package. The franchise villain was deeper and more pensive than ever before due to his time spent in the Sacred Realm following Ocarina of Time. As demonstrated at game's end, however, he wasn't afraid to use brute force if he needed. An important lesson to learn is never to underestimate children as Ganondorf literally got it in the head at game's end. Seeing King Daphnes drown with his kingdom was tear producing.
3. Majora's Mask-Majora's Mask is without a doubt the darkest Zelda game ever produced with one of the most sentimental stories in franchise history. All of the characters are extremely well developed and tied into the sidequests although ironically painfully ignorant of their fate at the end of the 3-day cycle. The Skull Kid is an allegory for the corrupting influence of society on children and Majora is an incarnation of pure evil. The ending scenes are some of the best in franchise history which is really saying something considering how high the franchise ranks in the overall videogame pantheon.
4. Twilight Princess-Despite all the hate it garners Twilight Princess is nevertheless an amazing title that deserves not only the Zelda namesake but also the higher "Teen" rating. While underutilized, Wolf Link is an intriguing concept nonetheless. Midna is without a doubt the greatest companion in franchise history. Also, taking a great nod from Ocarina of time, the number of dungeons and Epona rank right up there.
5. Skyward Sword-Don't get me wrong if you've seen my other thread posts, I love Skyward Sword. It lacks some of the fundamental elements i love to see in Zelda, however, The ocmpanion is weaker than expected, the overworld is disconnected, and the harp is almost ocmpletely defunct. Luckily, the great characters of Groose, Ghirahim, Demise, and Zelda as well as the excellent dungeons and ending ocme to the rescue.