This is the timeline that I agree with. It is called the Split Timeline Theory, and it is what many believe to be the actual timeline but Nintendo hasn't confirmed or denied anything. What it basically is that in OoT a two timelines are created when Link travels back in time to warn the people of Hyrule that Gannondorf isn't being honest about his pledge and preventing him from entering the Sacred Realm and the whole events of OoT from unfolding. In the timeline that he left The events of the Great Flood and TWW take place, because he didn't stop Gannondorf from getting into the Sacred Realm.

Notes:

• Thanks to Xykeb Zraliv for the hard text, and Hero of Time 87 for putting this together. And to ZP, for first exposing me to it.
• This is what I believe, feel free to make what you will of it.

          Creation of Hyrule and the Triforce
                           |
             Forgeing of the Master Sword
                  (Skyward Sword)
                           |       
                   Hyrulean Civil War
                           |
                    Imprisoning War
 Adult Timeline    (Ocarina of Time)  Child Timeline
            |        /             \          |
      The Great Flood                 Majora's Mask
              |                              |
      The Wind Waker              Ganondorf's Execution    
              |                              |
     Phantom Hourglass           Zant's Invasion of Hyrule  
              |                      (Twilight Princess)
       Link and Tetra find                   |
    and establish a new Hyrule.              |
              |                       Agahnim becomes a host for Ganondorf's soul.                                     
      Spirit Tracks                          |                     
              |                        War of the Wizard
              |                     (A Link to the Past)       
      War of the Bound Chest                 |
              |                       Revival of Ganon
       The Minish Cap             (Oracle of Seasons/Ages)     
              |                              | 
         Four Swords               Awakening of the Wind Fish
              |                       (Link's Awakening)        
   Four Swords Adventures          
                                    The Legend of Zelda
                                             |                 
                                One of the Zeldas is put
                                to sleep until Zelda II.