Skyward Sword's takes the cake for me, easily. Unless you include the dungeon from the Twilight Realm, which might not exactly be fair since the Silent Realms didn't get a dungeon- if the Silent Realms did get a dungeon... oh my gosh. That would probably be my favorite Zelda dungeon ever.
But the Silent Realms certainly more exciting, and the music always gorgeous when it was calm- and so easily caused me to jump when it switches. The layouts and scenery was all very fitting, too. Like a pleasant dream that can become a full fledged nightmare in moments.
The Twilight Realms were pretty boring, not sense of excitement, panic, or urgency. The Twilight Realm looks pretty cool, I guess... but the feeling is just so depressed. Although, that's what they were going for, but I prefer the overall "feel" of the Silent Realms. Also, bug collecting felt like a chore. The Silent Realms did not.