There are three rhythms on the Wind Waker. 3-time, 4-time, and 6-time. You set it to 3-time by just keeping the control stick in its normal position; you set it to 4-time by holding the control stick to the left; and you can set it to 6-time by holding the control stick to the right. You can control the notes played with the C-stick. The notes corresponded with the direction on the C-stick (meaning if you go right on the C-stick, you play a note to the right). Here are the songs that you can play on the Wind Waker: (I can't make it look like it does in the game right now, but keep checking back and one of these days it will look like it does in the game.)

WIND'S REQUIEM (3-Time)
Up - Left - Right

BALLAD OF GALES (4-Time)
Down - Right - Left - Up

COMMAND MELODY (4-Time)
Left - Normal - Right - Normal

EARTH GOD'S LYRIC (6-Time)
Down - Down - Normal - Right - Left - Normal

WIND GOD'S ARIA (6-Time)
Up - Up - Down - Right - Left - Right

SONG OF PASSING (3-Time)
Right - Left - Down