Pre-release and unused content

Before a game gets released you might see enemies and places that aren't in the released game, because they are taken out for unknown reason. The elements that were once in the game but were taken out are called Beta Elements.

Beta Elements
Here is a list of Beta Elements appearing in Mario games:

Super Mario Bros. 3
There were going to be two new enemies called Gold Cheep Cheep (a golden version of a Cheep-Cheep, and Green Parabeetles (green colored Parabeetles). The Gold Cheep Cheeps would come in groups and swim faster than regular Cheep-Cheeps and the Green Parabeetle is a green Parabeetle that flies faster than normal ones.

Koopa Troopas and and Hammer Bros. were going to host the mini-games. They were replaced by Toad. There were also different kinds of mini-games, similar to the ones in New Super Mario Bros..

Super Mario World
Dinosaur Land was drastically different, possessing an appearance similar to the various kingdoms of Super Mario Bros. 3.

There is also a hidden level in Donut Plains called "???" that unlocks a suit called "the Laser Suit". Nintendo even wrote a note at the beginning of the level. Source

Super Mario RPG: Legend of the Seven Stars
Looking into the coding of Super Mario RPG: Legend of the Seven Stars reveals several unused enemies (most of which seem to be unused sub-species), including a notorious one known as the Drill Bit.

Drill Bits seem to be related to Jabbits, and are recolors of them (which virtually confirms the fact that they would've been either stronger or weaker versions of them if they'd stayed in the game). Little is known about what role they would play in the game (or even why they weren't used), but it is known that they would say "This is for Yaridovich!" if Mallow attacked them with Psychopath superbly. Another instance of Drill Bit's surprising amount of publicity is that it was once listed in an old Nintendo Power guide. Drill Bit may be the most well-known unused enemy in any Mario game.

Interestingly, there are even some references to (and one appearance of) Drill Bit in the final game. Production of a Smithy Gang member called the "Drill Bit" was almost done at the time Mario fought the Manager, or so says one of his Pounder lackeys. Also, Drill Bit actually appears as one of the three enemies who tries to convince Smithy not to get too angry. A type of Machine Made Drill Bit even exists as a fight-able enemy in the final game. This Drill Bit is encountered when the Machine Made Yaridovich uses his Multiplier! attack, which lets him split into four gray Drill Bits. Drill Bits seem to have an ambiguous connection to Yaridovich, and some have suggested that the "actual" Yaridovich may have had a similar attack during a production stage of Super Mario RPG.

Super Mario 64
In the Beta version, it would've had a numbered health bar instead of the pointed one. Many stages and bars would be different. Thwomp would also have a scarier look and Mario would have a different jump (one that let him spin around after a triple jump in a way similar to the result of being hit by a Tweester in Shifting Sand Land). There would also be a tanish Cheep-Cheep. Mario was voiced differently (possessing a screechy, childlike voice rather than his current Italian accent) and Bowser sounded more tiger-like.SourceSource 2 and 3Source 4

Paper Mario
Early screenshots of this game showed that Poochy was going to play some sort of role in the game. Another screenshot showed that Nep-Enuts were going to be in this game also. Also the early version of Forever Forest showed that it would be much smaller, with all the forest's trees having sinister faces.

Yoshi's Story
It seems as if Flowers were going to appear in the game, which was once called by Yoshi's Island 64 Screenshot. Also, Big Guys were going to appear and Bone Dragons would be purple, flesh-covered dragons rather than bony, undead ones. Finally, Stage 4-2: The Jungle Puddle was known to be much scarier, with strange bubbles and a Bone Dragon.

Mario Kart 64
Kamek or a Magikoopa was going to be in this game playable, but got replaced by Donkey Kong. Also note that the Character Select Screen was going to be very different.

Super Mario Sunshine
In Super Mario Sunshine, Delfino Plaza is the main plaza of the game. However, in movies before release, it showed that there was going to be a different plaza (or possible prototype for Delfino Plaza), with a giant Strollin' Stu-like creature walking all over the place, and many more different things. A Human girl was going to appear here, wearing a pink dress. It is unknown whether she was important or not or what she was doing. She may have also been a citizen. Also FLUDD was going to be skinnier and Gooper Blooper was going to be dark blue and fought on top of the bridges of Ricco Harbor instead of in the market and helicopter area. Source

Mario & Luigi: Superstar Saga
Wario, Fox McCloud, Captain Olimar, Samus, an Excitebike Racer, and Link were going to show up in the Starbeans Cafe after Mario and Luigi made coffee, instead of E. Gadd (who was going to make an appearance, but only one).

Mario Power Tennis
In the intro of the game where Wario and Waluigi are drawing on the scorechart in the left the player can see Toad and Toadette's heads. It is unknown if they were going to be playable and they forgot to take their faces of the scorechart.

Paper Mario: The Thousand-Year Door
There were many unused badges. See Badges for information on them.

The partners from Paper Mario were going to appear but we're cut-off as well. Bow and Parakarry were the only ones left. There was also a strange robot-like creature.

Mario & Luigi: Partners in Time
In this game, there were going to be some Blooper enemies appearing in the Vim Factory wearing red shoes. While the screenshot only showed Luigi attacking one, it isn't known what their attacks were.

Super Mario 64 DS
Several beta screenshots were released for the game. Originally, all four characters could fight Bowser at the time and could fly. Most of these features were later turned into Mario-only abilities.

Super Princess Peach
The Koopalings were originally going to be in the game, but were taken out for unknown reasons. All of the Koopalings' lost sprites have been discovered by now. Oddly enough, Morton's sprites were spread around the internet long before those of his siblings.

New Super Mario Bros.
The working title for this game was Super Mario Bros. DS. Also, during early stages of production, Mega Goombas were going to be a generic species (the result of a Goomba colliding with a Super Mushroom and powering up) rather than an individual boss. There was also said to be a Mario and Luigi co-op mode at a time. Interestingly, an illustration of beta map icons still exists as a screenshot on page twelve of the final game's manual. There also was an underwater stage which also featured Manta Ray in VS. Mode.

Yoshi's Island DS
As stated below, Yoshi's Island DS was originally going to be compatible with Nintendo Wi-Fi. Also, one early screenshot showcasing a battle with Big Guy the Stilted seems to suggest that Big Guy was once going to be organic, as he had no patches on him in that picture (although one patch was visible near his right foot, which may merely mean his graphics were slightly incomplete). Finally, one screenshot of an unknown origin shows a Black Yoshi traversing a flowery area with Baby Peach. The particular event illustrated in the picture doesn't seem to be left in the final game.

Wi-Fi
Many Mario games were originally going to have Nintendo Wi-Fi; however, it was taken out of some. Mario Hoops 3-on-3 and Yoshi's Island DS (known as Yoshi's Island 2 back then) were the two games that were going to have Wi-fi.