Time Hole (to past)/ Super Mario Bros. Underwater

Shroob Castle

Battle

Victory!

Dark Dungeons

Shroob Castle

Serious Trouble

Spaceship Battle

Princess Shroob Battle / Overture to the End

Prince Bowser

Shroobs!

DESTROY!!

Elder Princess Shroob Battle / Overture to the End

Mutant Xenomorph Elder Princess Shroob / Final Battle

The Time Machine

Shrowser (this is not a final boss battle, it is actually an avoidence minigame)

Bye-Bye, Babies!

Old Ending

Credits

The End (Japan and PAL Only)

Which one is your favorite?

Time Hole (to past) / Super Mario Bros. Underwater

Gritzy Desert

Gritzy Desert (Smash Bros. Version)

Battle

Victory!

Koopaseum

Dark Dungeons

Serious Trouble

Thwomp Volcano

Professor E. Gadd

Thwomp Caverns

King Bowser

Prince Bowser

Bowser Battle

Shroobs!

Toad Town

Star Hill

Star Shrine

Shroob Attack

Shrooboid Brat / Petey Piranha / Mrs. Thwomp / Commander Shroob / Elder Shrooboid Battle

Time Hole (to present)

Which one is your favorite?

This is my Top 10 list.  If you disagree with this list, make your own in the comments!

10.) Kirby

9.) Lucario

8.) Charizard

7.) Donkey Kong

6.) Sonic

5.) Mega Man

4.) Samus Aran

3.) Mewtwo

2.) Bowser & Giga Bowser

1.) Captain Falcon

Which of the characters that I mentioned is your favorite?

Professor E. Gadd

Princess Peach's Castle

Time Hole (to past)

Time Hole (to past) / Super Mario Bros. Underwater

Toadwood Forest

Battle

Victory!

Serious Trouble

Vim Factory

Hammer Bros. Battle / Swiggler Battle

Yoshi Village

Yoob

Yoshi Mountain

Behind Yoshi Village (Remix of Yoshi Mountain)

Prince Bowser

Yoob's Belly

Kamek Battle / Sunnycide Battle

Time Hole (to present)

Which one is your favorite?

Main Title

File Select

Shroobs!

The Time Machine

Serious Trouble

Battle

Victory!

Professor E. Gadd

Time Hole (To Past)

Time Hole (To Past)/ Super Mario Bros. Underwater

Listen Up Now / Tutorial

Shroob Attack

Holli Jolli Village (Thanks a lot Nintendo for evilizing Jingle Bells!)

Prince Bowser

Bowser's Castle

Time Hole (To Present)

Peach's Castle

Which one is your favorite?

This is my top 20 list.  If you disagree with the list, then feel free make your own in the comments.

20.) Vs. Dialga / Palkia

19.) Palkia's Onslaught!

18.) Vs. Entei

17.) Vs. Lugia

16.) Vs. Suicune

15.) Vs. Raikou

14.) Vs. Giratina

13.) Shadow Lugia Battle

12.) Vs. Ho-Oh

11.) Arceus (same theme appears in all five mains series games)

10.) Vs. Ancient Pokemon

9.) Primal Dialga / Dialga's Fight To The Finish!

8.) Vs. Unova Legendary

7.) Regi Battle

6.) Vs. Reshiram / Zekrom

5.) Vs. Black Kyurem / White Kyurem (the battle themes for both Black Kyurem and White Kyurem are listed as separate, but I have yet to find a difference between the two battle themes)

4.) Xerneas, Yveltal, and Zygarde Battle

3.) Clash with Kyurem!

2.) Deoxys Battle

1.) Battle with Rayquaza

Which of the music that I've listed here is your favorite?