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In the Japanese and American versions of the 3DS' "StreetPass Mii Plaza", when attempting to purchase a DLC from a rabbit but then declining to buy it will cause the rabbit to depressively say "Oh, I see...". However, the European version removed the rabbit's depressed response and replaced it with a more neutral "Fair enough!", instead.

This was done to bring it in line with European laws put in place to prevent manipulating children into purchases; "Games should not include practices that are aggressive, or which otherwise have the potential to exploit a child's inherent inexperience, vulnerability or credulity or to place undue influence or pressure on a child to make a purchase."
Contributed by ProtoSnake
Holding the start + select buttons while booting an original Nintendo DS cartridge will load the game in its native resolution, rather than stretching it.
Contributed by Ganorith
On the "new page" screen of the internet browser on the "New 3DS", tapping the opening beat of the Mario theme, a stage select will appear which allows the player to access a version of Breakout with the website's URL address.
Contributed by noobheadz
In 2012 the Louvre museum in Paris, France, started offering 3DS museum guides. The purchase of the hardware was sponsored by Korean Air, and all the museum guides are branded with the airline's logo.
Contributed by snesiscool
Placing the AR Card on a colored surface during the AR Free Fishing game (available from the AR Arcade for 1 Play Coin) yields different effects based on the color. For instance, a blue background will display sardines, a green one will show green Koopa shells, and the red contains jumping Cheep Cheeps.
Making noise into the microphone while on the system settings screen will cause the icons to spin around the wrench. While doing this, the wifi helper icon can be seen on the back of the internet icon.
Contributed by Skarro
In the 3DS Sound app, when playing a sound file, switching to the Game & Watch Soccer background and pressing any button will allow you to take control and play the game.
Contributed by Skarro
If you blow into the mic while highlighting a 3DS application, the icon will spin around faster.
Contributed by Skarro