Arcade/Classic Era:
Characters:
-Sheriff (the main character from the arcade game Sheriff, a game and character that predates Donkey Kong)
Stages:
-Radar Scope
-Donkey Kong (the original level 1 level)
-Light Tennis/Color TV Game Collection
NES Era:
Characters:
-Mike Jones (Star Tropics/Star Tropics 2)
-Teddy (Mother)
-Little Mac (Punch-Out)
-Takamaru (Nazo no Murasame Jō)
-Nightmare (Kirby's Adventure)
-Medusa (Kid Icarus)
Cameos/Assists
-Diskun (Famicom Disk System mascot)
Stages:
-Devil World
-Excitebike
-Joy Mech Fight
-Tetris
-Balloon Fight
SNES Era:
Characters:
-Tin Star (from the game of the same name)
-Dion, Max and Jack (three person character) (Marvelous: Mōhitotsu no Takarajima)
-Hakkun (Sutte Hakkun)
-Lip (Panel de Pon)
-King K. Rool (Donkey Kong Country)
-Porkey (in his spider mech) (EarthBound)
-Poo (EarthBound)
-Samurai Goroh (F-Zero)
Stages:
-Battle Clash/Metal Combat
-The Devil's Machine/Giygas (EarthBound)
N64 era:
Characters:
-Saki Amamiya (Sin and Punishment)
-Master Hand (Super Smash Bros)
Stages:
-Sin and Punishment
-Doshin the Giant
-Andross/Planet Venom (the boss attacking from the background) (StarFox 64)
GameCube era:
Characters:
-Alexandra Roivas (able to transform into the other main playable characters) (Eternal Darkness)
-John Raimi (Geist)
Stages:
-Odama
-Battalion Wars
Wii era:
Characters:
-Captain Rainbow (from the game of the same name)
-Raymond Bryce (Disaster: Day of Crisis)
-Zip (FlingSmash)
-Playable Mii (probably wouldn't work if it comes out on a new Nintendo system)
Stages:
-Endless Ocean
GameBoy era:
Characters:
-Sabure Prince (Kaeru no Tame ni Kane wa Naru)
-Muddy Mole (Mole Mania)
Stages:
-F1 Race
-Solar Striker
-GameBoy Camera
Virtual Boy era:
Characters:
-Teleroboxer (the main robot from the game of the same name)
Stages:
-Red Alarm
GBA era:
Characters:
-Isaac (Golden Sun)
-Felix (Golden Sun)
-Stafy (The Legendary Starfy)
-Jill (Drill Dozer)
-Flint (Mother 3)
DS era:
Characters:
-Osu! Tatakae! Ouendan/Elite Beat Agents (tag team group of a various combination of characters from all 3 games)
-Hero/Heroine (Magical Starsign)
3DS era:
Stages:
-Steel Diver
Mario series:
Characters:
-Geno (Super Mario RPG)
-Fawful (Mario&Luigi series)
-Count Bleck (Super Paper Mario)
-Waluigi
-Tatanga (Super Mario Land)
-Captain Syrup (Wario Land)
Zelda series:
-Agahnim (Link to the Past)
-Majora's Mask/Skull Kid
-Tingle
-Vaati (Four Sword)
-Tetra/Toon Zelda
(along with Twilight Princess and Toon Link):
-Link (NES era)(uses attacks/items from Zelda 1 and 2)
-Link (SNES era)(uses attacks/items from Link to the Past and Link's Awakening)
-Link (N64 era)(uses attacks/items from Ocarina of Time and Majora's Mask) (aka the Link from Melee and classic)
Metroid series:
Characters:
-Ridley
-Dark Samus/Metroid Prime
StarFox series:
characters:
-Krystal (StarFox Adventures)
Stages:
-Dinosaur Planet
Pokemon series:
Characters:
-Mewtwo
-Deoxys
-Meowth
-Wes (Pokemon Colosseum)
3rd Party Chatacters:
-Namco: Pac-Man
-Hudson: Bomberman
-Capcom: MegaMan (classic series version)
-Square: Cecil (Final Fantasy 4)(has appeared in at least three versions of the same game on Nintendo systems)
Other Characters:
-I would personally like to see a brand new original character in the next Smash game, like a character that has an important role in the games story mode but has never appeared in a Nintendo game before it, Then after beating the story mode that character becomes playable.
I also think it would be cool if more characters had transformation abilities like Samus and Zelda. Like for example: Mario can turn into Paper Mario, Ganondorf can turn into Ganon from the NES/SNES games. Twilight Princess Link can turn into his wolf form.