One of the more interesting aspects of Legend of Zelda fandom is the debate on the timeline, if any, that the franchise follows. Go to any Zelda fan site and you are sure to find numerous theories pertaining to the order and nature of the timelines. Typically they fall into two major groups, linearists and splitists which means you believe that the timeline follows a straight order or that you believe that the timeline splits, usually focused around the ending of Ocarina of Time. I'm not sure if I need to explain this but the ending of Ocarina of Time involves Zelda sending Link back to the past to live his life and Ganondorf will never come to be while also leaving a future where Ganondorf was sealed in the Sacred Realm and such.
Here lets let the Angry Video Game Nerd explain:
Now to be entirely honest I don't spend a lot of time on timeline of the franchise. While it is certainly interesting to a point, to me the whole debate seems rather fruitless because I am not entirely convinced that Nintendo has put that much effort into. I mean I could be wrong and I'm certainly not telling fans to stop debating it but people really put their emotions into it. I've seen flame-wars over the topic and it is kinda startling.
But for the sake of argument, I'll presume that there is a timeline that the franchise follows and see what I come up with. Probably won't be anything new or original and I'm not doing any real research on the matter outside of what I know of the franchise and my own observations. If there is anything I need to be corrected on, please say so and I'll make a note of it.
What we know for sure is that there have been several Links, several Zeldas and only one Ganon/dorf. Also we know that Hyrule's landscape has changed dramatically but there are commonalities of towns and landmarks. There are only a few obviously direct sequels (in which the same Link stars) in the franchise as well, those would be:
LoZ/AoL, OoT/MM, Seasons, TWW/PH
Though if LoZ/AoL are indeed directly linked (no pun honest) doesn't it seem weird that there are two different Zeldas unless the Zelda in AoL is different than the one in LoZ but I dunno.
Of course this leaves 6 other LoZ games that feature an unique Link or at least not obviously connected Link. One game I'm kind of curious about is Link's Awakening. While not explicitly stated, to my memory anyways, I've always thought that the Link in that game was the same Link as the one in A Link to the Past but I also vaguely remember reading something in some video game magazine (I'm thinking Nintendo Power) that somehow the events of Link's Awakening takes place directly in the middle of Adventures of Link when Link takes the raft ride from the West to East continent but that seems unlikely to me.
But really the crux of the whole issue is OoT and how you interpret the ending. The Wind Waker takes place after the Ganondorf is sealed time but if Ganondorf was never to exist when Link is sent back to his childhood could Twilight Princess really have happened? Most people put Twilight Princess coming after that but now that I really think about it how could it? Sure Ganondorf is essentially presented as being a god in Twilight Princess so it is possible that he could enter any reality he chooses. With that being a possibility I suppose if I had to say the majority of the Zelda games take place in the Twilight Princess branch of the timeline.
But to be honest, as interesting as this is, I'm starting to feel like I'm rambling. My true feelings is that outside of the directly connected titles most Zelda games can be taken as their own stories with meta-styled references thrown in for the fans of the franchise. If there is a truly deeper connection, fantastic, but until proven otherwise I'm not going to think too deeply about it.