The only true connections are Ocarina of Time-Majora's Mask, Wind Waker-Phantom Hourglass-Spirit Tracks, The Legend of Zelda-The Adventure of Link, and Oracle of Seasons<->Oracle of Ages (these can happen in either direction). Because of the possibility of branching, WW cannot come after MM.
Sure, there may be things that connect the games in other ways, but there is no SET continuity aside from the ones I've listed. Minish Cap probably comes before OoT, but then there's the matter of Vaati, which brings up the possibility of branching paths. And then there's the questions. Are the Seven Sages in LttP the same ones from OoT? The towns in AoL are named after the Sages, so that means it takes place after OoT, but when? Is the raft shown at the end of the Oracle series the same one that wrecks in LA?
There is no official continuity to the Zelda series to connect all the games, nor will there be. Unlike other series, like Mega Man for example (as Zan knows all to well) there are no dates to connect them. One may be able to string together a rough timeline with uncertain dates, but nothing really sensible will work. Not to mention all the opposing arguments and timelines that could be created.
There is no way to create a cohesive timeline that has no branches, nor is there a way to create one containing all games.