The Wind Waker
Already out in Japan and set for an American launch in March 2003, the Wind Waker is looking to be the most story-based chapter yet. According to several interviews, it takes place 100 years after the end of Chapter 2 - placing it squarely between Ocarina of Time and Link to the Past. Hyrule has been flooded, and the majority of the land is totally submerged. It's currently unknown what Ganon's role in the game will be, or if he'll have one at all. It's rumored that he's trying to escape from the Sacred Realm by capturing the princess Zelda - which is why Link's sister is captured. Ganon may be ordering the capture of any girls with pointed ears, hoping that one of them will be the princess. I'll have a full chapter written up once I get the game for myself in March, so sit tight.
And I won't ruin anything else for you guys, but some things I've heard about TWW may completley shatter the idea of trying to create a coherent Zelda timeline. I'll try my best to rewrite and make sense of the whole thing when it comes out, but it's not looking good.
The Four Swords
I thought this multiplayer game included with the LTTP remake wouldn't have much of a story, but it seems I was wrong. Apparently Zelda is captured by Vaati the Wind Mage, and Link has to use the Four Sword to save her. The four sword splits Link into 4 separate entities that must work together to rescue the princess. Once I play through this, I'll determine if it's extensive enough to warrant its own chapter, or just an addendum to an already written one.
The End... for now