1.) Gusty Garden Galaxy - You start on a landmass floating in space. After a minute, a gust of wind blows you to another. Eventually, you'll wind up on the planet with the giant mole boss as a stage hazard. Don't worry, the stage resets after that.
2.) Tallon IV - Another changing stage. You start out in the landing site. After thirty seconds, the area scrolls in a varying direction. You follow the scrolling for a series of rooms until you wind up in another region. (Chozo Ruins if it scrolls left, Phazon Mines if it scrolls right, or Impact Crater if it scrolls down.) The scrolling starts after another thirty seconds and you're led through the different regions on the planet. Each area has a stage hazard, with the exception of Tallon Overworld. (Impact Crater = Metroid Prime, Phendrana Drifts = Sheegoths, Magmoor Caverns = Magmoors and lava, Phazon Mines = Space Pirates and Phazon.)
3.) Zelda's Throne - The area where you battle Zelda when she's possessed by Ganondorf. From Twilight Princess, obviously. Nothing too special about this place, other than demonic Zelda occasionally throwing bolts of magic into the arena.
4.) Mute City (Melee) - Is an explanation really necessary?
5.) Eagleland (Melee) - Again, another stage that should've been in but wasn't.
6.) Great Bay (Melee) - Oh, yeah.
7.) Princess Peach's Castle (Melee) - For some inexplicable reason, I miss this stage terribly. Therefore, it goes on my list.
8.) Dream Land (N64) - With updated graphics, obviously. But, come on. Who doesn't like this stage?
9.) Fountain of Dreams (Melee) - Why this wasn't in in the first place is beyond me.