The 3DS and Wii U eShops are slowly being cycled out of the system. Next year, credit card purchases will no longer work on these eShops, and once they become obsolete altogether, many games are likely to shoot up in value. Many 3DS titles are no longer being produced, so it's normal to see physical copies going for upwards of $50.
Finding DS and 3DS cartridges for purchase on eBay, Facebook, Amazon, and other online storefronts is something of a minefield. Gamers need to be careful, as there are many counterfeit products on the market. Copies of Pokemon games like the coveted HeartGold and SoulSilver are notorious for this. Be especially careful when purchasing games that don't come in their official packaging and boxes. But as far as legitimate games go, here are the most expensive physical complete-in-box 3DS games, not including the prices of loose copies.
Barbie: Groom and Glam Pups
This one is quite the enigma. At a consistent value much higher than any other plain 3DS title, Barbie: Groom and Glam Pups is priced at nearly $700 currently, which has actually dropped from its $900 value earlier this year. The Barbie game was originally made for the Wii and DS where it sold decently for kids, but the 3DS version looks to be incredibly rare, hence the high price. New and sealed copies can go for as high as $5,000.
Some fans believe that Barbie: Groom and Glam Pups' price tag is that most copies were destroyed by the publisher after it sold poorly. It's hard to tell whether or not this game is actually "worth" these prices in that it would seem like there's little demand for them aside from avid Nintendo collectors. However, one gamer says to have sold their CIB copy for $1,000 last year after it was only listed on eBay for about an hour.
Fire Emblem Fates (Special Edition)
The Special Edition of Fire Emblem Fates is a coveted item among gaming collectors. As Fates was originally released in multiple versions, the Special Edition includes all three storylines, Birthright, Conquest, and Revelation as well as an artbook. While used CIB copies hover between about $250 to $300 or even more than that, new versions of the Fire Emblem Fates Special Edition are sometimes listed for closer to $500. Even versions without the artbook can be sold for a high price, as it looks like much of the value comes with getting all three games in a bundle.
Frogger 3D
The 3DS installment of the old Frogger series is another unusual one, possibly due to low sales numbers and review scores, resulting in players discarding their copies and accruing a "rare" status. Much like its predecessor that released for the original PlayStation, Frogger 3D did poorly upon release, currently holding an average score of 54/100 on Metacritic, though there are only 11 reviews. While there's little data to go off of due to its rarity, new CIB copies of Frogger 3D can go for nearly $250, it seems.
Persona Q2: New Cinema Labyrinth (Showtime Premium Edition)
The sequel to Persona Q, Persona Q2: Shadow of the Labyrinth follows a combination of the characters seen in Persona 3, 4, and 5. The groups join forces and venture through movies and change films' conclusions to happy endings. As spinoffs, both games have done well, seeing generally favorable reviews among fans. The Showtime Premium Edition includes a collector's box, a plush, an artbook, a deck of playing cards, and a set of four buttons, and is valued at around $400 to $500 dollars on Amazon.