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I haven't seen anyone talking about the updated software sales on the investor relations part of Nintendo's website, so I went ahead and compiled all of the June 2016 figures and compared them to the March 2016 ones. Just as a reminder, these numbers are from April 1, 2016 to June 30, 2016, and the numbers reflect physical game shipments as well as digital sales.

Source: https://www.nintendo.co.jp/ir/en/sales/software/index.html

3DS Game: Total Sales: Quarterly Increase:
Pokémon X/Y 14.98M 280k
Mario Kart 7 13.56M 300k
Pokémon Omega Ruby/Alpha Sapphire 12.24M 400k
Super Mario 3D Land 10.81M 80k
New Super Mario Bros. 2 10.39M 140k
Animal Crossing: New Leaf 10.11M 110k
Super Smash Bros. for Nintendo 3DS 8.23M 110k
Tomodachi Life 5.09M 110k
Luigi's Mansion: Dark Moon 4.88M 60k
The Legend of Zelda: Ocarina of Time 3D 4.30M 260k
Wii U Game: Total Sales: Quarterly Increase:
Mario Kart 8 7.70M 200k
New Super Mario Bros. U 5.34M 150k
Nintendo Land 5.10M 30k
Super Mario 3D World 5.01M 190k
Super Smash Bros. for Wii U 4.90M 100k
Splatoon 4.42M 150k
Super Mario Maker 3.65M 130k
New Super Luigi U 2.64M 150k
The Legend of Zelda: The Wind Waker HD 1.82M 100k
Mario Party 10 1.81M 50k

 

Highest-selling award: Pokémon Omega Ruby and Alpha Sapphire with 400k

"Where'd that come from?" award: What made Ocarina of Time 3D sell so much this quarter?

Keep going award #1: Mario Kart 8 needs 1.06 million more to outsell Super Mario Kart (according to VGChartz)

Keep going award #2: Pokémon X and Y need 620 thousand more to outsell Pokémon Black and White (according to Nintendo shipment data)

Keep going award #3: Pokémon Omega Ruby and Alpha Sapphire need 480 thousand more to outsell Pokémon HeartGold and SoulSilver (according to Nintendo shipment data)

Pleasant surprise award: Wind Waker HD is ahead of Mario Party 10 again!

Fake-out award: Super Mario 3D World was not passed by Smash Bros, though they were just 20k apart last quarter.