I love Emerald's Battle Frontier Music. I also love the beginning music to Super Mario World Advance 2 when Mario is on a hot air balloon flying to Yoshi's Island. I also love the theme song to Dragon Ball Z Budokai 3 - that song rocks. I probably have so many more songs I like I just can't remember, lol.
Megaman 9 - Tornado man
Star Fox - Corneria
F Zero - Big Blue
SSBM - Dr. Mario theme
LoZ - Overworld
LoZ - Gerudo Valley
LoZ - Hyrule Field
SSBM - Fountain of dreams
SSBM - Mushroom Kingdom
The old Zelda theme is great, but lately the music in the games has been really mediocre. Nintendo really needs to step it up with the music and quit using the lame fake stuff and just go with a real orchestra.
Pallet Town song is awesome.
The song from Kirby Amazing Mirror and Squeak Squad... the song in the first "world"
Pokemon Silver title screen music <3 8-bit
Final Fantasy III theme song, don't ask me why