This will only work on the PAL version of the game.
First you need to make sure the game is set to 50hz. If it's set to 60hz then take your memory card out before you boot up the game, set to 50 and re-insert it at the title screen.
Load up your game or start a new one. In order to do the superjump you need to have a stick or a sword equipped but it will also work with a lightsaber. Start running in any direction and perform a running jump.
Right after you hit Triangle, hit Square. The timing needs to be exact or it won't work. You should see him fly farther and higher than he normally would. Keep practicing the jump, it will come in handy when you'll need to get to Yorda quick. You can also use the jump to skip major parts of the game.
You have to have completed the game at least once before you can get this ending. When Ico wakes up on the beach near the end of the game, go all the way over to where the cliffs are and continue up the beach. Along the way you should see a large rock and a couple of watermelons near it. Pick up one of them and proceed up the beach until you reach Yorda. You will now be treated with a slightly humorous end video but for some reason this does not work on the US version of the game.