The final trophy is Tamagon from Devil World, which is unavailable in the North American version without hacking or a cheat device. This trophy was completely deleted from the PAL version, despite the fact that Devil World was released in PAL regions.
Snooping around the insides of of the game 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.
One poking around the 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!"
Poking around the insides of the game has shown the names, at least, of seven removed characters: Mewtwo, Dr. Mario, Roy, Plusle & Minun, Dixie Kong, Toon Zelda, and Toon Sheik (the last of whom is speculated to be Tetra). 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, but are still accessible through hacks. These include Donkey Kong Jr., Dread Kong, and alternate character trophies for many of the playable characters.
This terrifying thing◊ is seen in the background in the Subspace Emissary. 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 suggest that several familiar enemies from the Kirby series, including Bronto Burt, Blade Knight, and Bonkers, were supposed to appear as enemies in the Subspace Emissary, 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.
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. Fairly be ye warned, however: Using Gameshark with Super Smash Bros.' for any reason permanently locks single-player mode into playing as Mario, which can only be undone by erasing all the game data.
Nintendo 3DS and Wii U:
The Ice Climbers were originally intended to be playable, but were cut from both due to hardware limitations in the 3DS version despite working fine on the latter.
Character icons for the Viruses from Dr. Mario are found in the Wii U version's data, apparently originally used as bosses for a Dr. Mario stage.
Version 0.9 of Super Smash Bros. Crusade includes several images of elements of the game that aren't actually in the game in this version, such as Classic mode. In addition, Pit's victory theme is present in the music folder despite Pit not being part of the character roster and several announcer lines are unused but still in the game's files. It is possible that these elements may be used in later versions of the game (Classic mode in particular has been confirmed for version 0.9.1).
A number of games in the series 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 King Of Fighters '96 with those moves enabled and edited into an useable state, 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 16-bit versions of UMK3 has Sheeva and Chameleon. While the latter is unfinished and only playable by hacking, Sheeva can be played by glitching in the SNES version.
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.
Going into the files for ''Mortal Kombat: Deception' and using a cheat device allows use of a lot of content that is either locked away and only viewable during the 'Konquest' mode or content that is dummied out completely. Quan Chi, Shang Tsung, Sonya, Jonny Cage, Jax, Onaga, Ghost Liu Kang, Younger versions of Shujinko, Monster (Fought during Conquest mode), Old Raiden, Kitana, Frost, Drahmin and Nitara are all playable in this fashion (with most missing special moves and all characters missing fatalities). Also, multiple stages used in Konquest mode can be hacked into the game as well as 'Puzzle Fighter' mini versions of every character (Including the dummied out characters) can be found and used in-game with cheat devices.
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.
One more for Budokai 3: At one point it was planned for every single playable character to have a story in Dragon Universe mode; this got fairly far into development, as there are English voice clips from some of these discarded ideas (like Krillin realizing that a lone surviving Saibaman is friendly, or Cell getting angry at one of his Cell Juniors for rebelling against him). The only vestige of these ideas in the final game is a line of dialog in Broly's story where Gohan says that Future Trunks warned them about him; Trunks having a run-in with Broly and leaving to warn the others was part of his storyline.
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.
Skullgirls was originally planned to have two endings for each character in the initial roster (except for Double): depending on a choice made after defeating the endboss, the player would receive either a good (or in most cases, bittersweet) ending, or a nightmarish bad ending. Limitations on development time and resources caused the choices and bad endings to be dropped from the game (and there are no plans to implement them with DLC characters), but the scripts for those endings can be found in the game's code.
Karin Kanzuki, 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 Doc Ock 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 game's 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.
Huitzil has several unused sprites across the course of the series, the most interesting being a half-finished arm ray gun super in the first game and a rudimentary animation for a combiner variant of his Final Guardian super in the second game.
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 Seong Han Myong remaining. Hacking reveals Bangoo (Rock's protégé), Vercci'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.
Tekken 3 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.
Later on, it was discovered that many more unfinished characters were hidden within the arcade version of Virtua Fighter. Among them were Siba, who was renamed "Majido" in-game, Jeff, a muscular soldier-like fighter, an early version of Akira who looks remarkably similar to the Mishimas in Tekken, and a male, boss-like character who uses most of Dural's assets save for his costumes (three of them, in fact). All of them (except for the latter, who uses Dural's) have an incomplete moveset thatare mostly based on the existing fighters and lack throwing moves. Several assests from beta versions were also found, including beta names for Jeffry and Lau, as well as data for an unused alternate character select screen.
Super Street Fighter IV originally planned to give some characters a second rival, according to some Ultra Combo videos, but despite this, they were stuck with their first rival for some unknown reason. Also, Arcade Edition had the newcomers Yun, Yang, Oni and Evil Ryu, all who have no rival cutscene; they just showed the intro of their opponent instead. However, Evil Ryu did have audio for the rival cutscene with Gouken in the game's files before it went unused.
The Japanese version of Marvel Super Heroes vs. Street Fighter has an unusual extra character from neither universe known as Norimaro, based on comedian Noritake Kinashi. He was dummied out from international releases, but evidence points to this being a very last-minute change, since not only was he not completely removed, around 90% of his graphics and dialogue were fully translated. Only his ending was overlooked, instead displaying text from Dan Hibiki's ending with Captain America's name tag.
The Gundam Battle Assault had a few characters removed in the two Playstation installments. In the original, the Mobile Suit Gundam ZZ Mobile Suit Hamma-Hamma was removed in favor of Wing Gundam, as Mobile Suit Gundam Wing was airing at the time. Using a Gameshark would allow you to reaccess it. In the second game, the Hamma-Hamma and Mobile Suit Zeta Gundam Mobile Suits Qubeley, The O and the titular Zeta Gundam were removed and data of the still-removed Hamma-Hamma was still left in. Again, Gameshark codes allowed players to reaccess them, though they didn't have pilots.