The end of Banjo-Kazooie featured footage of secret items hidden in the levels that would be used in Banjo-Tooie, with the ending promising said sequel would reveal how to get them. The plan was apparently to discover how to get the items in Tooie, go back to Kazooie to get them, then while the N64 is still on, take the cartridge out and put Tooie in, which would transfer them. This was supposed to take advantage of the fact that memory stayed in the N64's hardware for 60 seconds, but newer versions of the console cut this time down to 2 seconds, making the technique impossible and causing it to be scrapped. Instead, as a sort of consolation, you got the items in question by hunting down three Banjo-Kazooie cartridges in Tooie, cracking them open, and taking the items that fell out. Curiously enough, the Banjo-Kazooie Stop 'n' Swop things actually are accessible in-game, albeit only through a series of very long "codes" in the beach level that were practically impossible to find without hacking the code, as someone finally did.
Since Microsoft owns Rare, the series developer, both BK games are put on Xbox Live Arcade. Since both games are digital, Stop 'n' Swop actually saw the light of day, and they're compatible with Nuts & Bolts to earn parts and vehicles.
There's a level title hidden in Banjo-Tooie's code called "Ridiculously Secret Area". There's no actual area with that name, so the common belief is that Rare deliberately put the title in to throw off hackers.
In Symphony of the Night, there's a little trapdoor right when you enter the castle. You can glitch through it and find a vestigial level down there. It was later fleshed out to a full level in the Saturn release. The game code also contains recorded dialogue that isn't found in the game, apparently from an unused ending in which Maria turns into a demon.
There are audio clips of the voice actors (English and Japanese, at least) yelling "KONAMI!" with different inflections on the CD. It's pretty surreal.
Castlevania: Bloodlines for Genesis had dummied out levels, which were brought to public knowledge when a prototype cartridge surfaced. One of the levels took place on board a zeppelin.
Stinkoman 20X6 ever since Version 1 has had data for an enemy that looks like a cabbage. This is referenced in the Negative Zone level, a garble of sprites from all seven previous levels, where it finally makes an appearance.
There's a hidden palm tree inside the rocks near the bridge in the Bianco Hills level (from Mission 6 on). Similarly, in Delfino Plaza there's a extra Rocket Nozzle Box inside the belltower closest to the beach. (Shown here).
There's also a book and a door hidden in the structure at the bottom of the giant bottle in one of the red coin missions in Noki Bay.
There is a test room that contains a menagerie of unused objects, such as a soccer ball and rock blocks. Piantas and Nokis lurk this bizarre realm of numbered blocks and they all say the same placeholder error message. There's even an unused enemy◊, the same freakish walking Mook Maker onion from the earliest trailers of the game. Though due to the game not loading the model correctly, it instead takes on the appearance of some type of freakish walking banana◊.
Mega Man X8 might have been planned to have X, Zero, and Axl to be Navigators like their Distaff Counterpart. In the 2nd PC CD of it, you could find a folder of Japanese voice actors' sound data, including the main character's voice as Navigators(!). The idea seemed to be scrapped out because it would involve further scripting and scenarios. It's amusing to find that Axl feels very, very bored to have his job as a Navigator in his line.
Every single game of the Mega ManGame Boy (Rockman World) series contains unused music tracks. Many of them can be identified as alternate versions to existing tracks, most notably the ending themes to Wily's Revenge and MMII (the latter of which sucks a lot less than what you hear in the final game). MMV also contains two unused leftover tracks from IV.
Taito's little-known game Chack'n Pop features the first versions of Monstas and Mightas enemies found in Bubble Bobble (respectively, the purple whales and the white rock-throwing ghosts). The data found in the rom hinted that the Zen-Chans (the toy looking robots) were planned to appear as an enemy too, but were dumped from the final version for unknown reasons.
An unusual example: in Commander Keen: Aliens Ate My Babysitter, using a level warp code takes you to the now-playable high score screen, along with the message, "Keen is in the High Score screen. Call iD!" [the game's developer]. Well, you can imagine that the contest for which that was meant must have been scrapped really quickly!
The high score screen is also accessible via warp code in Keen 4 and 5, although you do not get a similar message. In all three games the high score screen has Keen running around the screen fighting enemies. Presumably the playable version was used by the developers to create the animation.
A similar example in another id Software game shows up in Wolfenstein 3D. In Episode 2, Floor 8, the entire western half of the level is occupied by a huge and nasty pushwall maze with multiple dead ends. In these dead ends are extra lives and some bosses. However, at one particular dead end is a floating sign which reads "Call Apogee — Say Aardwolf." This was intended to be part of a contest where a prize would be awarded to whoever found the sign and followed its instructions, but it was quickly scrapped when cheating and level-editing programs were published almost immediately after the game came out. Despite this, Apogee (now 3D Realms) still gets calls about it to this day.
Two very interesting things were removed at some point from Metroid Zero Mission. One was the ability to turn suit upgrades on and off from the pause menu, as in Super Metroid; fans are still wondering why this much-missed feature was taken out. (Cheat codes can turn it back on.) The second was... Crocomire! This Super Metroid boss was found in the ROM, with a full set of sprites and some movement code, but nothing else. It's possible to hack him into various rooms.
In turn, Super Metroid's ROM includes some interesting objects that were never used, most notably a "reflector" which would bounce any beam or missile off at a 90-degree angle.
In the original Metroid Prime, a variation of the intro can be found, featuring a narration by Samus herself (voiced by none other than Jennifer Hale). It was presumably removed due to Nintendo wanting to keep Samus as a Heroic Mime, rather than speaking directly to the player.
MP2 also originally was supposed to have Samus battle an Ing-possessed Luminoth. This one has an actual reason for being taken out: it's commonly stated throughout the game that a Luminoth would rather self-terminate than be possessed by an Ing.
Just to compete the trilogy, Metroid Prime 3was meant to have Samus' gunship be controllable, which the ship missile upgrades would presumably have been for.
If you bust out an FSB file extractor and the VGMStream program, you will find that Nicktoons: Globs of Doom, has several recorded voice clips that suggest that Dib would have got to fight GIR gone crazy and stuff again (The final game stuck you as Beautiful Gorgeous and Nicolai Technus for the boss battle); the clips perfectly describe every element of Zim's hijacked house that attack you in the battle.
Prince of Persia: The Sands of Time for the GameCube, PlayStation 2, and Xbox included remakes of the original game accessible through an in-game puzzle. The PC version left it out for some reason or another, but left the puzzle in place, minus the last step. You can actually see the secret door, but there's no way to get it to open.
Super Mario Bros. 3 is one of the more prolific examples of this on the NES. Numerous "lost levels" have been found. One consists of several unused variations of the empty white room with a giant question mark block that spits out three one-ups. Some contain Gold Cheep-Cheeps and Green Parabeetles, otherwise unused Palette Swaps. Several unused bonus games have been found; they all involve dice rolls, but no one knows what they're actually supposed to do, since all they do is roll the die, spit out some coins (which doesn't actually give Mario any coins), and then return to the map screen.
One of the box screenshots showed a level that was completely deleted from the final game, and another showed an alternate version of the World 1 map.
Titus The Fox has an array with room for 20 levels, only 16 of which appear in-game. Interestingly, the game is a reskinned version of a game called Moktar, which has a few of the missing levels (and misses a few others). The free one-level demo is another of the 20.
The first Crash Bandicoot (1996) game had a completely finished level called "Stormy Ascent" cut from the final version. The level resembles Slippery Climb in terms of design, only it's A LOT harder. The level was probably cut due to difficulty on account it's the hardest level in the original game and is probably the hardest level in the entire series.
Crash Twinsanity got hit with this HARD. Aside from the game feeling somewhat incomplete overall, the game had a few levels cut, at the very least a lava level and a cutesy level taking place inside Coco's brain were partially finished and programmed into beta builds. Cortex even lampshades it.
"Come now, as we explore a new dimension! It should have been two new dimensions, but we ran out of time..."
Crash Bandicoot: The Wrath of Cortex uses a few areas from early development and planted new levels on top of them. Ice Station Bandicoot for example uses a small platforming area as a background under the helicopter racetrack. An unused racing and dogfight level have also been found inside the game.
Full sets of brand-new sprites for all the Koopalings have been discovered in the data for Super Princess Peach, suggesting that they were at one point intended to appear in that game, presumably as bosses. By the time the game was finished, however, they'd vanished again.
The NTSC/UC PS2 version of Strawberry Shortcake: The Sweet Dreams Game has the full rendition of the song "How A Garden Grows" dummied out. The song is among the game data, but there is no conventional way to access it in-game.
In several of the Ratchet & Clank series, the developers took a lot of material that didn't make it into the finished game, and left it for the player to access in a secret area known as the Insomniac Museum. There have been three of these museums in the series so far (five counting the High Impact Games Treehouse in Size Matters and Secret Agent Clank), and although the first two (the second and third games) had sort of out-there methods of reaching them, the one in A Crack in Time just requires you to find all of the Zoni, then go and beat Vorselon again.
One truly Dummied Out level exists in the UYA Insomniac Museum. The south wall conceals a secret section of the museum, which can be seen jutting out of the building from the roof. It can be accessed using a glitch with the megaturrets to send you through the wall concealing it, revealing...a giant hallway that winds back and forth a few times, and when you reach the end, you die for no reason.
American McGee's Alice has Frog Footman and Fish Footman enemies and a strange 'Fungi' character (physically, a larvae-like creature with long skinny arms hanging from another inflated animal) that don't appear in the game proper, but can be spawned using console codes. There are also many unused lines, some of which were used in the sequel.
Several dummied-out areas can be found in Spyro: Year of the Dragon without a cheating device. It just takes some glitching skills.
Plok had three deleted levels, "Brendammi Bog", "Badream Fens", and "Breezy Beach". Like Sonic 2's dummied out levels, the graphics and/or layouts are unimplemented. There's also a vehicle test track.
In Bunny Must Die! Chelsea and the 7 Devils there are some dummied out items which seemingly do nothing - one is a stopwatch in the Chelsea & the 7 Devils mode, presumably this would be a time-stopper similar to Bunny's, another was a frog icon which may have been a mega-jump, a wheel icon which had no known or theoretical use, and a wand which was linked to a fireball attack that was also dummied out but used by a boss in the same game area.
There are several objects in the tile set which do not get used, including a sea floor, water graphics, and gray and gold objects.
Bunny had two other costumes which were dummied out - a pink one which may have been an upgrade ment for early on and a bright seafoam green one which was on the switch screen similar to the Busty Outfit and may have been the prototype.
In Atlantis No Nazo, a door in Zone 50 which leads to Zone 59 is inaccessible. This was possibly an oversight, but it makes Zones 59 and 55 impossible to reach without using a cheat code.
In Donkey Kong Land 2, an 8-bit version of the Boss Bossanova music (originally from DKC2) is in the game, but is never used. It was intended for use in some boss stages, but the Crocodile Cacophony music plays in all boss stages instead.
Donkey Kong Land was originally going to have different songs for Skyscraper Caper and for the final boss, but they're replaced for unknown reasons by "Balloon Barrage" and the normal boss music. Donkey Kong Land III has an 8-bit version of Rocket Rush, but again, it was never used.
Cave Story has an item called the Beast Fang, which can be made to appear in Yamashita Farm using a game editor. It seems to have no use — but then again, so do a number of the other items that do appear in normal gameplay. Pixel the Cat, the developer's avatar, is hidden in an inaccessible part of the Outer Wall, with a message for those who debugged the game when it was unfinished.