Shiek and Navi both mention the Shadow temple first, as does the OFFICIAL guide be Nintendo Power, so I'd say:
Forest, Fire, Water, Shadow, Spirit, Ganondorf
I usually do it in the order of favorite to least favorite, except spirit can't come before forest or water, and water can't be before forest, so I do
Ice Cavern, Fire, Forest, Water, Spirit, Bottom of the Well, Shadow, Ganondorf.
Also, the reason Saria mentions the Spirit Temple could be that either A. you haven't got the song of storms, or B. you already did the well, so you have nothing left as a child but that