Ok, i'm calling a little bit of personal bias on this one, cause I had a major crush on Nayru (the literal Oracle of Ages) after seeing her in this game. That being said, this is still a fantastic game and totally deserves to be on the list.
Easily one of the bigger risks Nintendo has taken with the Legend of Zelda games, Oracle of Ages (along with Oracle of Seasons) was actually made by Capcom. And to many's delight, they were awesome!
What struck me about Oracle of Ages was that they once again took the mechanic of time travel, and they made it their own, and made it totally different than Ocarina of Time or Majora's Mask. Watching time go back and forth through different uses of a harp was inspiring, especially since you could only do it in certain areas. Or, if you misplaced a jump, you'd be sent right back.
Also though, there was a surprisingly deep story focused around a Queen and her lost love, and her desire to build a castle to the sky. As you progressed through the game, it constantly cut back to the tower, and showed you how it was growing. Signaling that something was happening soon.
Oracles of Ages did a lot of things right, and because of that? It earns No.3 on my list.