Snooping around the insides of Melee revealed a few stages that didn't make it to the final game, including Ice Top (presumably another Ice Climber level) and Akaneia (which Fire Emblem fans should recognize). Neither are still in the game—loading Ice Top sends you to Icicle Mountain without music, and loading Akaneia causes the game to crash.
Poking around the insides of Super Smash Bros. Brawl has shown the names, at least, of seven removed characters: Mewtwo, Dr. Mario, Roy, Plusle & Minun, Dixie Kong, Toon Zelda, and Toon Sheik. Evidence suggests that none of them got particularly far into development outside of Mewtwo, who still has data referencing a Classic Mode portrait as well as a victory theme. This was later taken advantage of by the Project M developers as a springboard to put Mewtwo — and, later, Roy out of the same principles — back into full playability.
There are some trophies that have been dummied out of Brawl, but are still accessible through hacks. These include Donkey Kong Jr., Dread Kong, and alternate character trophies for many of the playable characters.
The code of the original Super Smash Bros. yielded two beta versions of Kirby's stage, Dream Land. The first is basically a simpler version of the stage, while the second is... something else. (Fun, though.) Fairly be ye warned, however: Gameshark and Super Smash Bros.' single-player mode do not get along so well.
One poking around Melee's Debug Menu can find Captain Falcon's "Come on! BLUE FALCON!" voice clip, which would only be used in Brawl seven years later. This confirms the claim that Final Smashes were intended to be implemented before Brawl. Word of God confirms they were planned since the first game, but time and memory constraints caused the development team to ax them in the first two games. This is further evidenced that not only is "Come on! BLUE FALCON!" within the first game's voice clips, but also Ness's "PK... STARSTORM!"
This terrifying thing◊ is seen in the background in the single-player mode of Brawl. It can't be fought, and it's the only one in the game. It was likely intended to be a recurring enemy of some sort, but was removed during development. However, there's a rare trophy that, while describing the thing as an enemy, makes reference to the captured specimen being the only known one.
Some unused files in Brawl suggest that several familiar enemies from the Kirby series, including Bronto Burt, Blade Knight, and Bonkers, were supposed to appear as enemies in the single-player mode, as well as Buzzy Beetle and Dry Bones from the Mario series. None of these actually made it into the game as enemies, though their models were used for a few of the trophies.
Many games have a lot of dummied out attacks for various characters, with some of them making their way to the sequels while others are forgotten about. They can be viewed with the help of a debug romset and it's easy to see why some of them were never put into any of the games (like for example the previous Big Bad Wolfgang Krauser, an extremely muscular man, doing a strange-looking cartwheel and then landing goofily on his belly), though some are sorely missed (Like the prototype Mu Shiki for Kyo and Deadly Rave for Geese.). Someone made a hacked version of the game and included those moves, you can see roughly what they'd look like in the game in their current form here.
Data has been found on the King of Fighters XII disk showing placeholders for pre-planned characters that for some reason couldn't make the cut; among them was Hwa Jai. The likely reason is characters being too incomplete to include (evidenced by the console exclusive characters Mature and Elisabeth, both of which have nigh-on useless movesets). XIII makes many of these characters a reality (Takuma Sakazaki, Vice, Mai, "Dark Ash" who turned out to be Saiki in Ash's body, and amazingly, Hwa Jai), up to and including Billy and classic Iori with flames.
The home ports of Mortal Kombat 4 had Kitana, who was scrapped from the final version, possibly in favor of Tanya. She was rather incomplete, having only a couple special moves and no fatalities, but she's fully playable in the N64 version. Also in the same game, there's a stage referred to as SKULL which can be accessed with a Game Shark code.
There's also Noob Saibot, who was dummied out in favor of Reiko, but is playable on the console version. However, like Kitana, he has limited special moves and, except for one (of three), no fatalities of his own.
A final character named Belokk was intended for the game, but was leaked before the team was ready, and was subsequently pulled. The only evidence of his existence, beyond the leaked photos, is a mysterious question mark that appears when you try to use the code to unlock Noob Saibot in the game over Tanya's picture, which doesn't do anything but was supposed to be where Belokk was.
In the arcade version of Ultimate Mortal Kombat 3, Rain was seen during attract mode, but completely inaccessable in-game. He was originally to be a joke (his name is "Rain" and his suit is purple), but was fully implemented in the console versions and Mortal Kombat Trilogy. The SNES UMK 3 has Sheeva and Chameleon. While the latter is unfinished and only playable by hacking, Sheeva can be played by glitching.
Hacking into Mortal Kombat Armageddon will pull up a list of inaccessible parts for Kreate-A-Kharacter, including options for staff and two-handed weapon styles.
Jump Ultimate Stars for DS has a number of dummied out characters that are actually accessible and (for the most part) fully playable with the use of cheats. This includes being able to play as the Komaman (training dummy), several incomplete (lack of sound effects, no Koma graphic) Support Koma like Sasuke and Freeza and the Game Breaker known as the Black Koma which grants Infinite SP to a player; obviously, that last one is abused by griefers online.
Naruto: Clash of Ninja Revolution has several unused sounds in its Sound Test. For example, there are sounds that imply that Lee originally went beyond two gates, Kisame calling out his Shark Skin, and another that implies that Gaara was intended to go Shukaku. The developers say that they left them in as Easter Eggs for the fans to discover. At least one, Itachi's "Mangekyo Sharingan!" was used in Clash of Ninja Revolution 2.
Players who checked the files for Dragon Ball Z Budokai 3 discovered a few things: announcer sound files that suggest that Android 19, Zarbon, and Dodoria (who appeared in the first Budokai but were absent from the rest) were to return, and perhaps most notably, a card and various sound clips indicating Bulma was to be a playable character. She even has a complete character model that appears in the game's training mode. As well, a bonus video included with the limited edition of the game shows Tiffany Vollmer (Bulma's voice actress) in the studio recording shouts for Bulma. Unfortunately, by normal means, she's not in the game. Using Action Replay codes on the Japanese version managed to yield her as an alternate costume for Videl, which is about as close to a playable Bulma as you can get.
The first Budokai, meanwhile, has dialogue recordings suggesting that Cui, Saibaman and Cell Jr. were planned. The former appears once in a cutscene in story mode and the other 2 are unplayable enemies. Though Cell Jr. and Saibaman showed up in Budokai 3 (but were extremely difficult to unlock), Cui didn't make the cut in any of the Budokais.
Budokai 3's unlockable voice clips show quotes from characters in story mode that are not actually viewable in ANY character's story modes, that suggest that several scenes and even entire story modes for some characters were cut. In particular, a few of Goku's suggest that Super 17 was going to be playable, or at least appear in his Dragon Universe mode as one of Goku's quotes is him saying "Hey, long time no see, 17!" in his gruff Super Saiyan 4 voice. Another for Vegeta suggests an alternate outcome to the fight with Kid Buu that involved Vegeta wishing for Goku's tail to grow back and Goku likely reaching Super Saiyan 4 as a result.
Sonic The Fighters had Honey the Cat, who was modeled after Honey in Fighting Vipers. Her data can be accesses by hacking the arcade version, but is almost completely gone from the version in Sonic Gems Collection. Furthermore, there also exists an unused Eggman form. All that is left is a pair of treads. If you hack the game, you can also play as "Rocket Metal" (which is a form of Metal Sonic that appears in the game's opening). A couple of unused tracks (including one for an unused level "Sunset Town") are also found inside the game.
Karin Kazuki, Sakura's rival from her Sakura Ganbaru! spinoff manga, was supposed to make her fighting game debut in Marvel Super Heroes vs. Street Fighter, much in the same way Shadaloo Cammy made hers in X-Men vs. Street Fighter. The sprites for Karin's fighting stance were already programmed into the game, although unlike the ones they actually used in Street Fighter Alpha 3, the Prototype Karin was simply a head-swap of Sakura with boots instead of sneakers, different gloves, and bicycle shorts instead of bloomers under her skirt. This video explains.
Marvel vs. Capcom 3 was originally intended to have 2 extra characters, Frank West and Dr. Octopus, in the game. Frank was removed due to supposed "RAM issues" whilst the reason for Dr. Octopus' disclusion is unknown. Hacking the game revealed their names as part of the character data, but nothing, no models, no voiceclips, no attacks, nothing was shown of them. Frank was brought back in Ultimate Marvel VS. Capcom 3 (probably revamped to be less RAM demanding), but Dr Octopus was still left out.
On another note, a Gamespot member hacked Ultimate Marvel VS. Capcom 3 and found a theme for an unused Okami stage, which was supposedly cut out due to not gelling with the games art style.
Darkstalkers: Huitzil and Pyron's endings from Night Warriors are actually in the first game but mostly go unused since they aren't playable. Hacking the game to play as them and beat the game as them will play their endings but with garbage text reading "AAAAAAAAAAA." They also have alternate player colours if selected with a different button.
Vampire Hunter 2 was made using Vampire Savior's engine, but with the Night Warriors cast. However, the new characters from VS remain as residual data, only their portraits remain...except Lilith, whose sprites and animations are all still present and functional. She can be selected by hacking and the game can be completed just fine if you use her, the only drawback being her lack of voice, victory BGM and that there's a chance the game might pit you against another Dummied Out VS character in arcade mode.
The console version of Soul Edge, (widely known as Soul Blade) was originally intended to have many unlockable guest fighters from people's endings, but the mechanic was scrapped with only Han Myong remaining. Hacking reveals Bangoo (Rock's son), Vercii's Ghost (Voldo and Cervantes' late friend), the Diver from Soul Edge's ending, Monkasei (Hwang's student, who was the inspiration for Yunsung in Soul Calibur II) and several others. Soul Edge was also supposed to feature Frederick Schtauffen (Siegfriend's late father) and Tanegashima (gunman from Mitsurugi's ending) but they were never implemented in time.
Tekken3 was at an early stage planned to include Jun and a salmon called Sake (a joke character) as PS1 exclusive characters. Jun's portrait was included in the game, but her character was just a standard Nina. Similarly, Sake was a standard Yoshimitsu. Jun was not included because the game makers wanted to include mostly new characters (which ultimately led to them beginning the mystery arc surrounding her possible death, a cornerstone of the series), and Sake was not included because it was considered too tricky to implement.
Virtua Fighter originally had a character named Siba who was in prototypes, but replaced by Akira. He was later playable in Fighters Megamix. Presumably, someone with an early arcade version of Virtua Fighter could hack it and find remnants of his existence, but they wouldn't be in any ports.