Yu-Gi-Oh!
There are several cards which feature Goemon characters, depicted in a non-comical fashion:

• Goe Goe the Gallant Ninja
• Ninja Grandmaster Sasuke
• Lady Ninja Yae
• Masked Ninja Ebisu.

There are also several cards that feature Sasuke as he appears in the Goemon games:

• Sasuke Samurai
• Sasuke Samurai #2
• Sasuke Samurai #3
• Sasuke Samurai #4
Contributed by Psychospacecow
The card "Vampire Hunter" is likely based off of the Belmont family from Castlevania. The castle from Castlevania is seen in the background of the card's art, and its translated Japanese name is Vampire Killer, the name of the Belmont family's whips.
Contributed by Psychospacecow
The card "Getsu Fuhma" is based on the protagonist of the Japan-only Famicom game released by Konami in 1987, Getsu Fūma Den.

"Ryu Kokki" is based on the last boss of the same game. In the game, it transforms two times (it has three forms), and the card illustration depicts its final form.
Contributed by Psychospacecow
Yu-Gi-Oh! is Japanese for "King of Games".
Contributed by Psychospacecow
The card Cosmo Queen is treated as a fusion card in Yu-Gi-Oh! Falsebound Kingdom and a Ritual Monster in
Yu-Gi-Oh! Duel Monsters II: Dark Duel Stories, Yu-Gi-Oh! The Duelists of the Roses, and Yu-Gi-Oh! The Sacred Cards.
Contributed by Psychospacecow
In Yu-Gi-Oh! Forbidden Memories, Yu-Gi-Oh! Duel Monsters II: Dark Duel Stories, Yu-Gi-Oh! The Sacred Cards, and Yu-Gi-Oh! Duelists of the Roses, Blue-Eyes Ultimate Dragon was treated as a ritual monster, summoned by a ritual card called "Ultimate Dragon". In the actual game, Blue-Eyes is summoned via the fusion of three "Blue-Eyes White Dragon" cards.
Contributed by Psychospacecow
The card Kuriboh's Japanese name roughly translates into "chestnut person". This is also the Japanese name for the Goomba creature from the Mario series.
Contributed by Psychospacecow
Sengenjin is treated as a ritual monster, utilizing a ritual summoning card called "Revival of Sennen Genjin", in the following games, when in actual fact it is a normal monster:
•Yu-Gi-Oh! Duel Monsters II: Dark Duel Stories
•Yu-Gi-Oh! Forbidden Memories
•Yu-Gi-Oh! The Duelists of the Roses
•Yu-Gi-Oh! Reshef of Destruction
•Yu-Gi-Oh! The Sacred Cards
Contributed by Psychospacecow
There are a series of Yu-Gi-Oh! arcade machines, originally used to introduce players to the Yu-Gi-Oh! 5d's anime.

As of September 28, 2012, there have been 7 Duel Terminals released in America and 14 in Japan.
Contributed by Psychospacecow