It has been confirmed that Skyward Sword, which is set to be released in late November, will have a second play through. Fans of the Zelda series will probably be reminded of the Master Quest or the alternate quest from the original The Legend of Zelda.
Details of this second playthrough are not yet available but it is supposed to be quite extensive.
On top of second quest, there will also be a boss challenge mode. This is again probably like the boss challenge mode from Ocarina of Time 3D.
Lastly, there will also be some kind of hint system that is comparable to the Sheikhan stones in OoT 3D.