Alrighty... I think I've come up with a good stage list.
I'm not too familiar with certain universes, though, so if I missed something, lemme know.
I'd also like suggestions for music for each stage.
[MARIO SERIES]
Good Egg Galaxy (Super Mario Galaxy)
Rogueport (Paper Mario: The Thousand-Year Door)
Peach's Birthday Cake (Mario Party)
Bowser's Castle (Super Mario Bros.)
Rainbow Cruise (Super Mario 64/Super Smash Bros. Melee)
Delfino Plaza (Super Mario Sunshine/Super Smash Bros. Brawl)
Luigi's Mansion (Luigi's Mansion/Super Smash Bros. Brawl)
Mushroom Hingdom II (Super Mario Bros 2/Super Smash Bros. Melee)
[DONKEY KONG SERIES]
Gangplank Galleon (Donkey Kong Country)
Timber Island (Diddy Kong Racing)
75m (Donkey Kong/Super Smash Bros. Brawl)
Kongo Jungle (Donkey Kong Country/Super Smash Bros. Brawl)
[YOSHI SERIES]
Yoshi's Island (Yoshi's Island DS)
Yoshi's Cookie (Yoshi's Cookie)
Yoshi's Island (Super Mario World/Super Smash Bros. Melee)
Yoshi's Island (Yoshi's Story/Super Smash Bros.)
[STAR FOX SERIES]
Krazoa Palace (Star Fox Adventures)
Fortuna (Star Fox)
Lylat Cruise (Star Fox/Super Smash Bros. Brawl)
Corneria (Star Fox 64/Super Smash Bros. Melee)
[KIRBY SERIES]
Mt. Dedede (Kirby's Dream Land)
City Trial (Kirby Air Ride)
Ripple Star (Kirby 64: The Crystal Shards)
Fountain of Dreams (Kirby's Adventure/Super Smash Bros. Melee)
Halberd (Kirby Super Star/Super Smash Bros. Brawl)
[MOTHER/EARTHBOUND SERIES]
Tazmily Island (Mother 3)
Twoson (EarthBound)
Onett (EarthBound/Super Smash Bros. Melee)
New Pork City (Mother 3/Super Smash Bros. Brawl)
[LEGEND OF ZELDA SERIES]
Death Mountain (The Legend of Zelda)
Lost Woods (The Legend of Zelda: Ocarina of Time)
Palace of Twilight (The Legend of Zelda: Twilight Princess)
Bridge of Eldin (The Legend of Zelda: Twilight Princess/Super Smash Bros. Brawl)
Pirate Ship (The Legend of Zelda: Wind Waker/Super Smash Bros. Brawl)
Great Bay (The Legend of Zelda: Majora's Mask/Super Smash Bros. Melee)
Hyrule Castle (The Legend of Zelda/Super Smash Bros.)
[METROID SERIES]
Phaaze (Metroid Prime 3: Corruption)
Tourian (Metroid)
Norfair (Metroid/Super Smash Bros. Brawl)
Frigate Orpheon (Metroid Prime/Super Smash Bros. Brawl)
Brinstar (Metroid/Super Smash Bros. Melee)
[POKEMON SERIES]
Realgam Tower (Pokemon Colosseum)
Sky Pillar (Pokemon Ruby/Sapphire)
Celadon City (Pokemon Red/Blue)
Spear Pillar (Pokemon Diamond/Pearl/Super Smash Bros. Brawl)
Poke Floats (Pokemon Series/Super Smash Bros. Melee)
[FIRE EMBLEM SERIES]
Sacaean Plains (Fire Emblem)
Kingdom of Daein (Fire Emblem: Path of Radience)
Castle Siege (Fire Emblem Series/Super Smash Bros. Brawl)
[F-ZERO SERIES]
Mute City (F-Zero Series)
Port Town Aero Dive (F-Zero GX/AX/Super Smash Bros. Brawl)
Big Blue (F-Zero X/Super Smash Bros. Melee)
[RETRO SERIES]
Underworld (Kid Icarus)
Infinite Glacier (Ice Climber)
Gyromite (Gyromite)
Flat Zone 3 (Game & Watch Gallery)
Flat Zone (Game & Watch/Super Smash Bros. Melee)
Summit (Ice Climber/Super Smash Bros. Brawl)
Skyworld (Kid Icarus/Super Smash Bros. Brawl)
[STANDALONE SERIES]
Hall of Heiroglyphs (Wario Land)
WarioWare, Inc. 2 (WarioWare: Mega Microgame$!)
Valley of Repose (Pikmin)
Venus Lighthouse (Golden Sun)
PictoChat (Nintendo DS PictoChat/Super Smash Bros. Brawl)
Panel De Pon (Puzzle League Series)
Smashville (Animal Crossing/Super Smash Bros. Brawl)
Battlefield
Final Destination
[THIRD PARTY SERIES]
Dr. Wily's Castle (Mega Man)
Dracula's Castle (Castlevania)
Space Colony ARK (Sonic Adventure 2)
Zanzibar Land (Metal Gear)
Shadow Moses Island (Metal Gear Solid/Super Smash Bros. Brawl)
Green Hill Zone (Sonic the Hedgehog/Super Smash Bros. Brawl)
[MARIO]
Good Egg Galaxy- Obviously going to be tournament banned because it would need weird physics, but it would be a fun stage to play on. Definitely good for casual smashers.
Rougeport- Which area, of Rougeport? If there's going to be a Paper Mario stage, I think the Glitzville arena would be better.
Peach's Birthday Cake- This is actually the first stage I though of when somebody suggested a Mario Party stage. I'm cool with it, though it would probably be tournament banned.
Bowser's Castle- Yes.
Rainbow Cruise- A favorite stage of mine. Though I'm like one of the negative two people who like it, I'd still like to see it in
Delfino Plaza- Also a favorite stage of mine.
Luigi's Mansion- I think they need to revamp the stage from what they had in Brawl. Maybe the rooftop area of the mansion as the stage would be good.
Mushroom Kingdom II- Nah. It wasn't a very good stage to begin with.
[DONKEY KONG]
Gangplank Galleon- Doesn't Toon Link's stage satisfy this?
Timber Island- A Diddy Kong Racing stage would be cool, but I don't think Timber Island is the best choice for this.
75m- Good for nostalgia, and a fun stage to play on. Just not good for tournaments.
Kongo Jungle- Why not? It's a good stage
[YOSHI]
I'm not going to respond to all of these specifically, but I say we just keep in the stages that have already been made for Yoshi. Maybe a Baby Bowser's Castle stage though. That would be a blast.
[STAR FOX]
Kroazoa Palace- Definitely. It would be a fun stage.
Fortuna- Don't really remember enough about Fortuna to give a good response.
Lylat Cruise/Corneria- Keep them both in. They're good stages.
[KIRBY]
Mt. Dedede- Don't know enough about the game to give a good response.
City Trial- Yes. This stage would be really fun. Maybe it could have an alternate as one of the arena battles once in a while.
Ripple Star- I don't remember the game well enough to give a good response.
Fountain of Dreams- I always likes this stage. Bring it back, is my vote.
Halberd- I like this stage. Keep it in.
[EARTHBOUND]
I really don't know anything about this series.
[ZELDA]
Death Mountain- Maybe a Dodongo's Cavern stage, but not a Death Mountain stage.
Lost Woods- Nah. It would be to hard to turn this into a good stage.
Palace of Twilight- That would be a cool looking stage, but not necessarily a good stage.
Bridge of Eldin- Keep it.
Pirate Ship- Keep it.
Great Bay- I'm not sure about this one. It felt like a filler stage to me.
Hyrule Castle- Yes. This was the best stage in the original SSB. Also, the tornado hazard was always fun.
[METROID]
I don't know enough about Metroid to answer.
[POKEMON]
I love Pokemon, but honestly, all I think we need is Pokemon Stadium stages. Stages outside of that would just feel a bit gimmicky. Maybe, just maybe, we could get a Gym stage.
[FIRE EMBLEM]
I don't know enough about Fire Emblem.
[F-ZERO]
I agree with every stage you suggested and don't really have any other opinions on them.
[RETRO]
Underworld- Definitely a good stage idea. It would be better than Skyworld.
Infinite Glacier- Maybe it could replace the Mario Bros. stage. It would still have the same look to it, but it wouldn't be as cheap.
Gyromite- R.O.B. needs a stage.
Flat Zone 3- Meh. We really only need one Flat Zone stage.
Flat Zone- See Flat Zone 3
Summit- Yay?! It was a fun stage. Keep it in.
Skyworld- Change the stage. I mean, I want a Skyworld stage, just not how it was in Brawl.
[STANDALONE]
We need WarioWare, Pictochat, an Animal Crossing stage, Final Destination, and Battlefield. That's pretty much it for these.
[THIRD PARTY]
Dr. Wily's Castle- Assuming Megaman gets in, either this stage or a Netbattle arena would be good.
Dracula's Castle- Assuming a Castlevania character makes it, Dracula's Castle would be a cool stage.
Space Colony ARK- I'm actually leaning more towards a Chao Gardens stage, but an ARK stage would be cool too.
Zanzibar Land- I don't know enough about Metal Gear to answer.
Shadow Moses Island- I liked the stage, and it's important to the Metal Gear universe. This needs to get in
Green Hills Zone- Yay nostalgia?! I want this stage in.