
Basically I believe in three timelines overall. One forked although internally consistent with itself, while the other two are linear with some inconsitencies that can be mostly handwaved.
The first timeline I regard as the Miyamoto Timeline. I disagree with the notion that Miyamoto cares nothing about the timeline or that he doesn't know what he's talking about. As per 1999, this what the timeline was before Eiji Anoma too the helm:
OoT-->ALttP/LA-->LoZ/AoL
There's some inconsistencies with OoT not matching up perfectly with ALttP's backstory and Ganon being dead at the end of ALttP but ALttP is before Loz because it's about the ancestors of LoZ's Link and Zelda and OoT is about Ganondorf's first rise and fall and his first tranformation from a human thief to the Demon King he's known as in the 2D games. Also, the creators have also mentioned that the town names in AoL are supposed to refer to Sages of OoT. So basically a somewhat consitent timeline.
Then there's Eiji Anoma Timeline.
OoT-->(adult)-->Flood-->TWW/PH-->ST
OoT(child)/MM-->TP
Everything before OoT is still canon, though their placement along with everything else post OoT has yet to be touched on. OoT was used to support a timeline split, which would have been a perfect opprtunity to retcon in a new timeline involving TWW without destroying the old timeline. But then came along TP which does nothing support that the old games have anything to with Eiji's new Timeline. You could argue that ALttP could fit after TP since the Master Sword being in a bunch of ruins that once was the Temple of Time within a heavily wooded area shows a transition between the Mastersword being in the Temple of time at the end of OoT and within Lost Woods in the begining of ALttP. That may be so, but TP itself does an even worse job of being a prequel to ALttP. Ganon's dead at the end the full Triforce is never in his possession. Compared to that, the Sacred Grove scene just seems like a thematic connection, nothing more. You might as well say the Twilight Realm is the Sacred Realm since when you first enter it and look back, the gateway you you just traveled through looks like it was literally ripped from ALttP's artwork.
For now, I consider TP "spiritual prequel" since if I was forced to chose where ALttP could fit, there's no other place I'd put it. Certianly not after TWW. St clearly shows Old Hyrule is gone for good and ALttP is clearly Old Hyrule. What bugs me though is what to with LoZ/AoL. TP introduces a totally different set of Sages than the ones in OoT. We never learn their names and since the events of OoT's adult future never happen, it seems unlikely they're the same ones from OoT. If so, how could the towns be named after the Sages in OoT if they never became Sages in the Child Timeline. If I had to place the LoZ games anywhere, I'd be more inclined to place it along with TWW's end of the timeline split because that's the one where the OoT Sages are revered. Anyways, only a minor nitpick since it's possible the ones in TP share the same names as their OoT counterparts, or this is form they took since Ganon didn't block them from acheiving Sagehood like he did in OoT. *shrug*
Next is the Four Sword Games.
TMC-->FS/FSA
Which deal with the Light Force and Vaati instead of the Triforce and Ganon. Numerous allusions are made to both the old and new timelines but none give any chronological reference nor do the help bridge the two timeline. In FSA Ganon upsurps Vaati's title as the Big Bad and the Triforce is alluded to at the end, making it seem like the Four Sword games proceed even OoT despite featuring Ganon as a villain. The creators do say they place the Four Sword games rather early in the timeline. On the other hand, if you seperate the Old and New Timeline, you could argue that the Four Sword games assume OoT's former posistion as ALttP's prequel. However, until stronger evidence can be found, I treat these connections as purely spiritual.
Lastly I have the Oracle games, which I have no idea where to place. Most people place it between ALttP and LoZ which helps bridge the gap somewhat, but in OoS, the soldiers that were suppose to escort Din refer to themselves as Hylians, which are a dead race except within the Royal Family by the time of ALttP. Chronoloically that should place the Oracle games sometime after OoT or TP but well before ALttP. I suppose the writers meant to say Hyrulean, which would be their nationality instead of ethnicity.
All in all my timeline looks more like this:

As you can see, the chronological connections are pretty straight forward, whereas spiritual connections are all over the map. I think the latter is the source of all confusion in timeline theorizing which is why I stick to connections that are purely chronological. If no such connection exist between two games, then they exist in separate, albeit just as canonical, timelines.
Edit: Come to think of it, OoX would be the perfect bridge between the 3D and 2D games if it comes between TP and ALttP. It fits with Ganondorf's deleted extended speech about returning someday which could have been an allusion to Twinrova ressurecting him in OoX. If only it was more clear what happened to the Triforce at the end of TP. Link and Zelda still have their peices but Ganon's just sorta fades away. If OoX is to be believed perhaps Link and Zelda obtain Ganon's TOP offscreen sometime between just after the battle with Ganondorf and the scene at arbiter's grounds.
Edited by SOAP, 24 November 2010 - 10:13 PM.