Star Fox Adventures began development as Dinosaur Planet, which originally began development as a direct sequel to Diddy Kong Racing, starring Timber the Tiger (who himself was intended as the main character of DKR when it was Pro-Am 64, before Donkey Kong characters were incorporated into it). It was pitched as an adventure/racing hybrid where Timber, equipped with a rucksack, little fingerless gloves, and a baseball cap would go back in time and team up with a younger version of Tricky, a boss from the first DKR. Wizpig, the main antagonist and final boss of the first Diddy Kong Racing, was also involved. It would seem a working title for this iteration of the game was "Dino Island", going by several posts on former Rare employee Ed Bryan's Twitter account.
Eventually it was decided to rework the concept into an entirely new original IP with no story connections to DKR and two new main characters, named Sabre and Krystal, and also make it a full-on action-adventure game directly inspired by The Legend of Zelda: Ocarina of Time. DP/SFA's various racing segments are said to be remnants of the original DKR successor concept, and while he retained the name of the DKR boss (something Rare seems to regret), Tricky would wind up becoming his own distinct character. Several files within DP/SFA's data also mention Timber, obviously a remnant from when he was the star.
Sabre and Krystal were in turn eventually replaced by Fox McCloud as the main playable character when the game was rebranded into what we know today as Star Fox Adventures, though Tricky would remain as his sidekick and Krystal would remain as a main character.
A few of Banjo-Tooie's worlds were originally planned for its predecessor, Banjo-Kazooie, such as the fire side of Hailfire Peaks and Glitter Gulch Mine. Many of these were cut primarily because of time constraints.
Gobi mentions leaving for the "Lava World" in Click Clock Woods, which adds up as Gregg Mayles' concept art for the cut lava world shows that Gobi would have been present. Gobi would eventually live up to his promise by appearing in the fire side of Hailfire Peaks in Banjo-Tooie, after being freed in Witchyworld.
Early in development, the layout at the top section of Brink Terminal where the secret entrance to the tower is was different compared to the final build of the game. The tower itself was absent and a pond with rails was originally placed at the plaza where the dance pad is set in the final build of the game.
Plok! was originally envisioned as a coin-operated arcade game titled Fleapit, running off of Rare Ltd's Razz board, which was never used in a released game.
Chris Sievey, the actor behind the popular 80s UK comedy character Frank Sidebottom, had agreed to voice Plok in the game before its cancellation. The SNES game would not have any voice acting whatsoever outside of digitally-made grunts and laughter.
Plok! was at one point going to feature an items shop, which would've been run by an anime-styled character named Suki. While the character wasn't used, Plok creators John and Ste Pickford kept her in mind for future installments that never came to be, but Ste was ultimately happy Suki never appeared in a Plok game as he felt that Western attempts to replicate the stylings of anime rarely turned out well.
Dragon Rock, Star Fox Adventures' final SpellStone area, was considerably larger and more complex in earlier versions of the game than in the final release. Both the leaked December 2000 build of Dinosaur Planet and also the E3 2002 kiosk version of Star Fox Adventures show that Dragon Rock featured a slew of additional areas that didn't make the final cut, such as an underground quarry area where Sabre/Fox would have to save the imprisoned EarthWalker from being eaten by a group of creatures known as Skeetlas, and also a large underground mining facility Sabre/Fox could only access by flying the imprisoned CloudRunner to the top of the titular Dragon Rock (a giant tower in SFA) at the center of the map. In SFA's case, Fox would have to solve a puzzle that would involve powering the portal at the back end of the room that would grant him access to Drakor, Dragon Rock's boss.
In the final release, both the underground quarry and the mining facility were removed: Fox simply frees the EarthWalker from a corral on the surface by hitting a switch located nearby the imprisoned HighTop from across the map, and Fox immediately skips to fighting Drakor after being dropped off by the CloudRunner at the top of the center tower. Funny enough, when Fox lands on the platform in Drakor's arena, it bizarrely shows electricity spewing around him, which was a remnant of the portal he was supposed to activate in the cut mining facility segment in order to access the boss.
The SFA dev team admitted on a 2003 Rare Scribes that Dragon Rock was massively scaled back from its intended design due to "approaching deadlines", presumably referring to the impending Microsoft buyout in 2002. It's worth pointing out that the mining facility area can actually be found in the files of the final retail release of SFA and surprisingly in a much more complete state than the kiosk's version, which indicates that the dev team continued working on this area in the final months of development but ran out of time to polish it to their liking.
Much like the original Star Fox on Super Nintendo, Star Fox 64's stages are split into three difficulty routes: Easy, Normal and Hard. However, unlike the original, SF64 only features two versions of Venom, one for the Easy Route and one for the Hard Route, the latter of which is where the Star Fox team has a final rematch with their rivals, Star Wolf.
It turns out the development team had planned on including another variation of Venom for the Normal route, where Fox McCloud would jump out of his Arwing and battle Andross on-foot with a bazooka. According to the staff, this was scrapped due to time constraints. The pilot mode option seen in Star Fox 64's battle mode is actually the repurposed remnants of this idea.
The telephone line level of Grimace's Birthday was supposed to have energy running through the cables as a hazard, but this was objected to by McDonald's and replaced with a squirrel Grimace could bounce off of.
Inside the code for the SNES version of Daze Before Christmas are a set of mostly Christmas-related quotes and messages:
Any dramatic game the producers want us to take seriously as a representation of contemporary reality cannot be taken seriously as a representation of anything -- except a game to be ignored by anyone capable of sitting upright in a chair and chewing gum simultaneously. -- Richard Schickel (slightly modified)
... Now you're ready for the actual shopping. Your goal should be to get it over with as quickly as possible, because the longer you stay in the mall, the longer your children will have to listen to holiday songs on the mall public-address system, and many of these songs can damage children emotionally. For example: "Frosty the Snowman" is about a snowman who befriends some children, plays with them until they learn to love him, then melts. And "Rudolph the Red-Nosed Reindeer" is about a young reindeer who, because of a physical deformity, is treated as an outcast by the other reindeer. Then along comes good, old Santa. Does he ignore the deformity? Does he look past Rudolph's nose and respect Rudolph for the sensitive reindeer he is underneath? No. Santa asks Rudolph to guide his sleigh, as if Rudolph were nothing more than some kind of headlight with legs and a tail. So unless you want your children exposed to this kind of insensitivity, you should shop quickly. -- Dave Barry, "Christmas Shopping: A Survivor's Guide"
I stopped believing in Santa Claus when I was six. Mother took me to see him in a department store and he asked for my autograph. -- Shirley Temple
During the prerelease of Nickelodeon All-Star Brawl 2, a set of placeholder pages were found on the game's website relating to different characters. Most notable of these pages was one for Helga, a character who was in the first Nickelodeon All-Star Brawl and hadn't been seen in All-Star Brawl 2 marketing materials or leaks at that point - this led a lot of fans to believe that Helga would be returning. Ultimately, she would only be a background cameo on the Aquarium stage.
A scrapped feature in Daze Before Christmas was a Street Fighter style battle against Anti-Claus, which supposedly was "[argued] about at length" by the development team.
Rocko from Rocko's Modern Life was intended to appear as a playable character in Nicktoons MLB but was scrapped for unknown reasons, with the only remnants of his appearance being his skeleton and a small black square labeled as his texture. Rocko's Modern Life is the only Nickelodeon show without a playable character to be referenced in the opening copyright credits.
In early stages of development, the game had a "RUSH" mechanic that would increase based on the amount of tricks the player performs in a combo. It's currently unknown what purpose the "RUSH" served during gameplay.
The 3DS version of Imagine Babyz has unused content pertaining to what seems to be an unreleased 2D shoot 'em up titled Sound Rider. There is a title screen, multiple ship and bullet sprites, and two MOD tracker-styled songs.
Alongside Garfield, Rocksteady from Teenage Mutant Ninja Turtles was originally going to be one of the two post-launch playable fighters in Nickelodeon All-Star Brawl - notably without his partner-in-crime Bebop, much like Michelangelo and Leonardo's inclusion without Raphael and Donatello. He was ultimately replaced by Shredder, and all that remained of his inclusion at launch was a placeholder stock image and the codename "hunter".
Rocksteady would eventually become playable in Nickelodeon All-Star Brawl 2.
Big Bumpin' was originally an adaptation of the Sumo minigame from Fuzion Frenzy, where characters would push one another around inside caged metal zorb balls. However, Burger King wanted all of the mascot characters to be visible in gameplay, leading to the game being reworked into a dodgems game as you could see the characters' heads.
Traveler's Tales had intended to slide a Christian Easter egg into Toy Story 2: Buzz Lightyear to the Rescue!, inserting a sticker on a suitcase reading "JOHN 3:16", a citation for a Bible verse reading:
"For God so loved the world, that He gave His only begotten Son, that whosoever believeth in Him should not perish, but have everlasting life"
When Disney saw it, they insisted that it be removed, so in the final game the sticker simply reads "NY CITY".
An unused battle model of Edelgard's Hegemon Husk exists within the data of Three Hopes, as seen with the head that now matches her Three Hopes design it is an original model made for this game.
As the cutscenes in the game are all pre-rendered, and that is the only time we see Hegemon Edelgard in Three Hopes, it is speculated that the seen where she transforms may originally have been a boss fight.
Despite being playable in Fire Emblem: Three Houses, Gilbert, Anna, Cyril, Hanneman, and Alois all have recruitment flags (the internal value which tells the game if the unit is in your army or not). They lack any skills or data assigned to them however and trying to deploy these units or use them in battle with crash the game.
Interestingly, Gibert is not referred to by his real name nor is he sorted to be with Kingdom characters despite his role in the Three Hopes story. However Alois is always sorted to be next to Jeralt and Byleth in the menu, rather than with the Church like in Three Houses.
Within the game, there exists a model of a generic Hero class found in the training grounds in the later half of the game, and class data for an unused Hero class exists within the game that can be loaded in.
It uses the generic attacks of the 'Mercenary' Class but lacks the animations for it's class action despite having 2 meters for it, suggesting that it was meant to be a promotion for the class rather than Swordmaster being the sole promotion to Mercenary.
War Monk, Dark Flier, and Valkyrie also exist within the game's code, but they're in an extremely unfinished state as they lack a Sprite, Model, Text, and any functional abilities. They do however have Class Stat bonuses assigned to them, hinting that at one point they were considered to be brought back.
Note: it is speculated due to Holst's in-game lore and his character design that he was originally designed to canonically be in the Hero class and not the Swordmaster class like he is in the final game, this is however just speculation.
A few of Banjo-Tooie's worlds were originally planned for its predecessor, Banjo-Kazooie, such as the fire side of Hailfire Peaks and Glitter Gulch Mine. Many of these were cut primarily because of time constraints.
Early in development, the layout at the top section of Brink Terminal where the secret entrance to the tower is was different compared to the final build of the game. The tower itself was absent and a pond with rails was originally placed at the plaza where the dance pad is set in the final build of the game.
Plok! was originally envisioned as a coin-operated arcade game titled Fleapit, running off of Rare Ltd's Razz board, which was never used in a released game. 
Plok! was at one point going to feature an items shop, which would've been run by an anime-styled character named Suki. While the character wasn't used, Plok creators John and Ste Pickford kept her in mind for future installments that never came to be, but Ste was ultimately happy Suki never appeared in a Plok game as he felt that Western attempts to replicate the stylings of anime rarely turned out well.
Dragon Rock, Star Fox Adventures' final SpellStone area, was considerably larger and more complex in earlier versions of the game than in the final release. Both the leaked December 2000 build of Dinosaur Planet and also the E3 2002 kiosk version of Star Fox Adventures show that Dragon Rock featured a slew of additional areas that didn't make the final cut, such as an underground quarry area where Sabre/Fox would have to save the imprisoned EarthWalker from being eaten by a group of creatures known as Skeetlas, and also a large underground mining facility Sabre/Fox could only access by flying the imprisoned CloudRunner to the top of the titular Dragon Rock (a giant tower in SFA) at the center of the map. In SFA's case, Fox would have to solve a puzzle that would involve powering the portal at the back end of the room that would grant him access to Drakor, Dragon Rock's boss. 
Much like the original Star Fox on Super Nintendo, Star Fox 64's stages are split into three difficulty routes: Easy, Normal and Hard. However, unlike the original, SF64 only features two versions of Venom, one for the Easy Route and one for the Hard Route, the latter of which is where the Star Fox team has a final rematch with their rivals, Star Wolf.
In early stages of development, the game had a "RUSH" mechanic that would increase based on the amount of tricks the player performs in a combo. It's currently unknown what purpose the "RUSH" served during gameplay.
The 3DS version of Imagine Babyz has unused content pertaining to what seems to be an unreleased 2D shoot 'em up titled Sound Rider. There is a title screen, multiple ship and bullet sprites, and two MOD tracker-styled songs.
An unused battle model of Edelgard's Hegemon Husk exists within the data of Three Hopes, as seen with the head that now matches her Three Hopes design it is an original model made for this game. 
Within the game, there exists a model of a generic Hero class found in the training grounds in the later half of the game, and class data for an unused Hero class exists within the game that can be loaded in.