My theory on the Zelda timeline is that there is one timeline..
Remember in Ocarina of Time **spoilers ahead!**
.. where Zelda and Impa were fleeing from Hyrule and Zelda threw the Ocarina into the moat? Link picks it up and events in Ocarina of Time happen as they did, but in the ending, when Zelda transports Link back in time, maybe he has to collect the 3 Spirit Stones again, only when Link gets the Ocarina, he gets a different telepathic message, thus leading him into the events of Majoras' Mask (which wasn't that good of a game, imo).
But to stay on the topic of Mario: There is no timeline for the Mario games like there is for the Zelda/Metroid games.. the only games that seem to be in some order are Yoshi's Island, Donkey Kong, and Mario Bros.