The biggest retcon by far (and the only game placement-related one) was when WW kicked LttP out of its place as sequel to OoT. From then until HH, it became a difficult game to place since we couldn't be sure how many of its ties to OoT were forsaken. Finally, the retcon was completed when the HH told us exactly how LttP still follows OoT.
Sleeping Zelda is no longer the original Zelda, if she ever was. That was rejected right when LttP was released.
MC is no longer where the hat tradition started, if it ever was. Replaced with SS (with room for the tradition starting much earlier).
I believe that the Temple of Time has been canonically moved to the woods, even in the OoT-era.
The MS was no longer created by the Sages. (unless they were around before SS and helped Hylia with the Goddess Sword?)
OoT retconned much of the IW, though that continued to be retconned as described above. It is now no longer the first time the Triforce is discovered.
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In an effort to induce some discusson... With the possible exception of WW, I think most of these were smart moves, merely showing an oversight in the original works. For example, Sleeping Zelda made it virtually impossible for more than one game to precede LoZ. It was important to abandon this tale in order to open up the timeline to more thought-out ones. Lately they've been trying to make them more vague so they don't have to repeat this in the future - that is, they need only add, not contradict.
@several posters above: Retcon and canon apply to story, not gameplay. Dungeon style and linearity aren't "canon" elements.