1 One Who Bares Fangs At God - Xenogears
2 Heavy Metal - Henry Hatsworth in the Puzzling Adventure
3 Smithy Phase 1 - Super Mario RPG
4 The Last Stand - Chrono Trigger
5 Dancing Mad - Final Fantasy VI
6 Chasing Gary - Bully
7 Emperor Ing - Metroid Prime 2: Echoes
8 Hopes And Dreams/SAVE The World - Undertale
9 02 - Kirby 64
10 Megalovania - Radiation's Halloween Hack
The Contenders
11 U.N. Owen Was Her? - Touhou Project 6: Embodiment of Scarlet Devil
Though not technically the final boss since it's in an extra stage, Touhou 6 is incredibly short anyways with only 7 stages so I'd say it counts. Touhou Project is the series to always have consistently amazing music, and there's a reason why this song has earned its place as one of the most well known Touhou songs along with Night of Nights and Bad Apple; it's that amazing. Unlike both of those this song is not a remix, so I guess you could say it's the most popular actual Touhou song. Either way though, it's great, I highly recommend you give it a listen.
12 Battle Against The Masked Man - Mother 3
13 Master Hand - Super Smash Bros 64
14 Golden Diva - Wario Land 4
15 Your Best Nightmare/Finale - Undertale
Every music in undertale is overrated, fanbase sucks a lot!
16 Last Battle - Cave Story
Cave Story's music is incredible and this is definitely not an exception. It's hard for me to pick a favourite song from this game, but I can definitely say this one's up there as one of the best, and that's saying a lot!
17 Zanza The Divine - Xenoblade Chronicles
18 The Highlands (Combat) - Borderlands 2
19 Hero's Pass (Combat) - Borderlands 2
20 Giga Bowser - Super Smash Bros. Melee
21 Crocodile Cacophony - Donkey Kong Country 2: Diddy's Kong Quest
22 Veldin In Peril - Ratchet & Clank
23 Big Bad Baby Bowser - Yoshi's Island
24 Final Boss (JP) - Sonic CD
25 Awakening - Xenogears