No problem, I'm glad I could help! If you're looking for anything else, just let me know!

I think that Rak's answer had cleared up doubts about WW being in the child timeline, but it seems more clarification is needed. In 2002, Aonuma and Miyamoto sat down for an interview. The both confirmed a split timeline AND confirmed that WW takes place in the adult timeline. Here's the important quote from that interview:
"Ocarina of Time basically has two endings of sorts; one has Link as a child and the other has him as an adult. This game, The Wind Waker, takes place a hundred years after the adult Link defeats Ganon at the end of Ocarina."

If you want to read more, I'm sure you can find it somewhere on the internet, like Zelda Wiki. Also, here's a list of Japanese translations so yours won't be lost anymore: http://forums.legendsalliance.com/index.php?showtopic=17108

Hey Scarlet! Your question is one that a lot of theorists struggle with. While James did answer with one theory, there is another prominent one out there. The ending of MM does suggest that Link does leave to return to Hyrule (entering the Lost Woods and all that jazz). But there is a theory that suggests he doesn't make it. He gets lost in the Lost Woods and becomes the Hero Shade in TP (since he knows all the moves and is passing them on to TP Link).

Also, in regards to MM Link being TP Link's father, I doubt that's true. Most of the games are explicit when they are linked to previous games in the series. I'm sure that the dialogue would have mentioned something about a father-son relationship or at least strongly implied it.

I think that Rak's reply to Waker of Winds will help you answer some of those questions. A lot can be cleared up by looking at the original text (the Japanese text, that is). A really good place to find these is here: http://forums.legendsalliance.com/index.php?showtopic=17108

I really like this article! I think it's cool when writers look farther into games! Keep posting stuff like this!

I don't want to step on any toes, but I don't think Trevor's question was answered completely:
"Well what did adult Link do in the Wind Waker timeline? You see in the intro of WW that he left Hyrule, but for what? Do you think it’s possible that the Zelda Wii game could fill that blank in?"

Adult Link didn't do anything in the WW timeline after OoT. If you recall, Zelda sends him back to the past when he's child Link. Since there is only one Link, he continues in the child timeline with MM.

In Wind Waker, the King of Red Lions says this: "Once, long ago, he defeated Ganon and brought peace to the Kingdom of Hyrule... A piece of the Triforce was given to the Hero of Time and he kept it safe, much as Zelda kept hers. That sacred piece is known as the Triforce of Courage. When the Hero of Time was called to embark on another journey and left the land of Hyrule, he was separated from the elements that made him a hero. It is said that at that time, the Triforce of Courage was split into eight shards and hidden throughout the land." At least, that's what NoA put in WW. The Japanese translation says, "Long ago, the Hero of Time defeated Ganon and restored peace to Hyrule. He had a Triforce dwelling in him just like Zelda. It was called the Triforce of Courage. It is said that when the Hero of Time traveled through time and left Hyrule, he was separated from the source of being a hero and the Triforce of Courage turned into 8 fragments and scattered throughout the land."

This translation is much more clear in stating that it was his travel back to the time when he was a child that separated him from the timeline where he was the Hero of Time. He had to choose between being an adult and a child, that's why he left Hyrule.

This means that there is not a Link in between OoT and WW in the adult timeline, there's no game. Otherwise they would be directly contradicting WW.

Also, I just want to clarify something that James said in his response to EzloSpirit: "The Adult Timeline follows into the Wind Waker and Phantom Hourglass, where Ganondorf was imprisoned and left powerless by what Zelda and Link did to him." He was not actually powerless. If you'll recall, the end of OoT, he says, "When this seal is broken.... That is when I will exterminate your descendants!! As long as the Triforce of Power is in my hand...." That means he still has the Triforce of Power, he's not powerless.