Exertainment Mountain Bike Rally & Speed Racer
While both of these games individually aren't rare at all, the combination cartridge was only sold with an exercise bike that worked with Super Nintendo games. As a result, you can expect to pay nearly $4,800 for this one cartridge.
Amazing Tater and Spud's Adventure
This is a weird one. Atlus, a company known for localizing obscure Japanese games, released several on the Game Boy, none of which sold well. The rarest of all were Amazing Tater and Spud's Adventure, which each go for nearly $2,000 now.
The Virtual Boy was Nintendo's attempt at a portable virtual-reality console in the 90s, and it was pretty much universally panned by everybody. Virtual Bowling had the distinction of not only being the last game released for it, but also only being released in Japan, making it super rare. Expect to pay around $2,000 for a copy.
Yoshi's Story: International Edition
Nintendo wanted stores to be able to show off Yoshi's Story to customers ahead of its actual release in the US, so they sent a bunch of them copies that worked on North American N64 systems but were still in Japanese. Of course these became collector's items, and now sell for upwards of $1,200 online.
Clayfighter: Sculptor's Cut
Unlike Hagane, which was incorrectly labeled as a Blockbuster exclusive, this enhanced edition of a mediocre N64 fighting game absolutely was exclusive to the rental chain, meaning the only way to get one was to buy the copies the chain inevitably sold off. Just the cartridge will set you back nearly $400, while a boxed one can go for as high as $4,000!
The singularly rarest video game of all time. Bandai released it along with an interactive exercise mat, but Nintendo immediately asked them to recall it so they could sponsor the idea and produce even more. The result was the Nintendo Power Pad, and the game was re-released as World Class Track Meet, but this meant that only about 200 copies of the game were sold before it was recalled. A copy was recently sold online for a whopping $35,100!