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 Betas 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, similiar 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 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. There would also be a tanish Cheep-Cheep. Mario is voiced differently and Bowser sounds 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.

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 we're going to be in the Starbeans Cafe after making coffee, instead of E. Gadd.

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 Princess Peach
The Koopalings were originally going to be in the game, but were taken out for unknown reasons. Morton's sprites are the only remains from the beta version of that game.

New Super Mario Bros.
In this game, back then, this game was going to be called Super Mario Bros. DS. In this game, Mega Goombas were going to be species, not only Bosses and there was going to be a co-op Mode. Also in the Instruction Manual of the game in Page 12 you can see a Beta Screenshot of the game.

Wi-Fi
Many Mario games were originally going to have Wi-Fi however was taken out. 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.