In A Link to the Past, Link defeats Ganon and is able to take the Triforce for himself. His wish is that the effect of Ganon's evil actions are reversed, thus restoring Hyrule (the and Sacred Land) to its former glory.
In Wind Waker, during the final showdown, Ganondorf is moments away from touching the Triforce, but the King of Hyrule beats him to it. The King wishes that the old land of Hyrule is submerged forever under the waves of the Great Sea, and that Link and Tetra can lives their lives in the new world above the ocean. As the wish is granted, Ganondorf is thrown into a fit of rage and attacks Link. However, Link is able to counterattack and deals the final blow to his archnemesis, killing Ganondorf for the last time (in that particular timeline, anyway).
In Skyward Sword, Link is able to combine the Triforce as well. His wish is the destruction of Demise. As a result, the Goddess Statue on Skyloft breaks free and falls to earth, crushing the villain's seal and killing him. Unfortunately his servant, Ghirahim, kidnaps Zelda immediately after and travels back in time to when his master was still alive. He uses Zelda in a ritual that unseals Demise, thus subverting Link's wish.