New Super Mario Bros. Ultimate

This could be the ultimate Mario game. The stages are based off Super Mario Bros. 3, Super Mario World, Super Mario Galaxy & more.

World 1: Mushroom Kingdom

 * Tatanga

World 2: Subcon

 * Reznor
 * Birdo
 * Mouser
 * Tryclyde
 * Fryguy
 * Clawgrip
 * Wart (End Boss)

World 3: Dark Road

 * Mack
 * Bowyer
 * Yaridovich
 * Exor
 * Culex
 * Smithy (End Boss)

World 9: Poisoned Swamp

 * Wario & Waluigi

Super Mario 64 (1996, N64)
 * Big Bob-omb - A giant Bob-omb in Bob-omb Battlefield. He appears as the first boss in the game, and the first star.
 * Whomp King - A giant Whomp on top of Whomp's Fortress. He appears as the first star, and after he is defeated, there is a tower on top of the fortress.
 * Big Bully - Two of these giant Bullies appear in Lethal Lava Land. On both occasions they try to knock Mario into the lava.
 * Eyerok - Two stone hands with eyes on their palms. They appear when the player blasts open the top of the Pyramid in Shifting Sand Land and ride the elevator inside.
 * Big Boo - A giant Boo which appears three times in Big Boo's Haunt. He initially appears once all the Boos in the mansion have been removed, again in the underground Merry-Go-Round, and lastly on the top balcony of the mansion (possibly what inspired Boolossus).
 * Big Mr. I - A giant Mr I which only appears in the attic of Big Boo's Haunt.
 * Wiggler - A giant Wiggler, which becomes angry when his home in Tiny-Huge Island gets flooded.

Paper Mario (2000, N64)

Super Mario Sunshine (2002, GCN)
 * Polluted Piranha Plant, huge Piranha Plants made out of sludge. Defeated by simply squirting water into their open mouths. They appear in Delfino Airstrip and Bianco Hills once, and three times in Delfino Plaza.
 * Petey Piranha, who appears in two of the episodes of Bianco Hills.
 * Gooper Blooper, who appears in two of Ricco Harbor's episodes and one of Noki Bay's.
 * Wiggler, who resides on Gelato Beach as the boss of the third mission, angry at Mario for disturbing his nap.
 * Mecha-Bowser, a giant mechanical version of Bowser, controlled by Bowser Jr. Appears only in the first episode of Pinna Park.
 * Monty Mole, who shows up in two levels, both times arming a large, triple-gun cannon that fires Bullet Bills, Missile Bills, Bob-ombs, and Glorpedoes.
 * Phantamanta, the silhouette of a giant manta ray appearing in Sirena Beach that splits into smaller manta rays when sprayed by F.L.U.D.D.
 * King Boo, who only appears in Sirena Beach's Episode Five.
 * Eely-Mouth, who has taken up residence under Noki Bay and is unwittingly poisoning the water with purple sludge.
 * Shadow Mario/Bowser Jr., who, although causing the whole island's issues, never actually is the boss of a level, besides every level's one Shadow Mario chasing mission.
 * Bowser, the final boss of the game, is found sitting in a hot tub full of green sludge floating in the skies of Corona Mountain. Bowser Jr. and Princess Peach are found with him.

Mario & Luigi: Superstar Saga (2003, GBA)

Mario & Luigi: Partners in Time (2005, NDS)

New Super Mario Bros. (2006, NDS)

Super Mario Galaxy (2007, Wii)
 * 1) Dino Piranha ×2
 * 2) King Kaliente ×2
 * 3) Mandibug Stack x1
 * 4) Bugaboom ×1
 * 5) Megaleg ×1
 * 6) Kamella ×3
 * 7) Tarantox ×1
 * 8) Topmaniac ×4
 * 9) Bouldergeist ×2
 * 10) Major Burrows ×2
 * 11) Baron Brrr ×1
 * 12) Undergrunt Gunner ×3
 * 13) Kingfin ×1
 * 14) Fiery Dino Piranha ×1
 * 15) Bowser Jr. ×1
 * 16) Bowser ×3

Super Paper Mario (2007, Wii)

Mario & Luigi: Bowser's Inside Story (2009, NDS)

Super Mario Galaxy 2 (2010, Wii)
 * 1) Peewee Piranha ×2
 * 2) Giga Lakitu ×1
 * 3) Digga-Leg ×2
 * 4) Gobblegut ×2
 * 5) Mandibug Stack (miniboss) ×1
 * 6) Bugaboom ×1
 * 7) Rollodillo ×1
 * 8) Sorbetti ×1
 * 9) Megahammer ×2
 * 10) Glamdozer ×1
 * 11) Squizzard ×2
 * 12) Prince Pikante ×1
 * 13) Boomsday Machine ×2
 * 14) Whomp King ×1
 * 15) Fire Gobblegut ×1
 * 16) Giant Bowser ×3
 * 17) Dino Piranha ×4
 * 18) King Kaliente ×4
 * 19) Major Burrows ×3
 * 20) Bouldergeist ×2
 * 21) Fiery Dino Piranha ×2

New Super Mario Bros. U (2012, Wii U)
 * Boom Boom (Tower)
 * Sumo Bro (Tower)
 * Kamek (Tower)
 * Lemmy Koopa (Acorn Plains)
 * Morton Koopa Jr. (Layer Cake Desert)
 * Larry Koopa (Sparkling Waters)
 * Wendy O. Koopa (Frosted Glacier)
 * Iggy Koopa (Soda Jungle)
 * Roy Koopa (Rock-Candy Mines)
 * Ludwig von Koopa (Meringue Clouds)
 * Bowser Jr. (Airships)
 * Bowser (Peach's Castle)

Super Mario 3D World (2013, Wii U)
 * Bowser ×3 (as Meowser ×1)
 * Boom Boom ×3
 * Pom Pom ×3
 * Hisstocrat ×3
 * Boss Brolder ×3
 * King Ka-Thunk ×2
 * Prince Bully ×2
 * Motley Bossblob ×3

Mario & Luigi: Dream Team (2013, 3DS)