Luigi's Mansion

While waiting on the control screen for around 3 minutes, and the song will play in a jazzier style. Getting the groove, Nintendo?

 

Animal Crossing (From GCN to 3DS).

There are 2 ways to find this song. Listen to the track "K.K. Song", or wait on the "Island with members loading" theme for at least 2 minutes in Animal Crossing New Leaf. Oh, and "K.K. Song" is basically Totaka's Song on repeat!

 

Mario Kart 8

You can only hear this with MKTV, or Mario Kart Television, but sometimes blue Yoshis will hum the song. Super hidden and super cute! You can also hear music from Animal Crossing in the main track itself, near Tom Nook's Store.

 

Yoshi's New Island.

Wait on the World 6 selection screen for at least 3 minutes, maybe more, maybe less, and the song will play.

 

Tri-Force Heroes

NOTE! This isn't about Totaka's Song. Why is this game on the list then? There is a special ball where you can play up to 23 different songs from past Zelda games!

 

Pikmin 2.

In the Gamecube version of this game, if you wait on the cave complete screen for about 2 and a half minutes, the hidden song will play.

 

Mario Paint: Artist's Studio

Another Japanese-only release, in one of it's starting videos, the first section of Totaka's Song is used while an elder woman is walking across a street. (Sorry, no picture.)

 

Yoshi's Touch and Go!

It's hard to find, but once you reach 1000 yards (Mountains)! in hard mode, pause the game and wait, the song will play. Talk about hard to find!

 

Possible: Wii Sports.

Many people say they hear Totaka's Song with the tennis rackets's hits. It is only what they hear in their head, however, while searching for secrets like this one.