EDIT: This thread is for the blue button Sky3DS. The new Sky3DS+ (with orange buttons) is supposed to play all these games.
Nintendo implemented a new Anti-Piracy measure to their latest games this fall, which prevents the games from being played with a Sky3DS. It is very likely that all upcoming 1st party games have the new AP (and it looks like 3rd party games will have it as well). However, all the games released before this fall still work with a Sky3DS, so the flashcart is not worthless. I will keep this list updated as more games with AP appear.
The following games do not work with a Sky3DS (starting from latest releases):
Mario & Luigi: Paper Jam Bros.（马里奥与路易RPG：纸片马里奥MIX）
Monster Hunter X（怪物猎人X）
Chibi Robo! Zip Lash（转转小机器人）
New Style Boutique 2: Fashion Forward (note: JPN version works)
Pokemon Super Mystery Dungeon（口袋妖怪 超不可思议的迷宫）
Stella Glow (note: JPN version works, english translation available through HANS)
Horse Life 4
Hello Kitty And The Apron Of Magic: Rhythm Cooking (note: JPN version works)
Barbie And Her Sisters: Puppy Rescue
Shovel Knight
Thomas And Friends: Steaming Around Sodor
The Legend of Zelda: Tri Force Heroes(塞尔达三角力量英雄）
7th Dragon III Code: VFD（第七龙神3 代号VFD）
Goosebumps: The Game
Picross 3D 2（立体绘图方块2）
Animal Crossing: Happy Home Designer（动物之森 快乐家园设计师）
Fire Emblem If - Special Edition（火焰文章if特别版）
Fire Emblem If - Anya Oukoku（火焰文章if暗夜王国）
Fire Emblem If - Byakuya Oukoku（火焰文章if白夜王国)
EDIT: There might be games that I missed, so if you notice that a game is missing, please inform me about it. Should this be a sticky post by the way? It's quite common question.

任天堂实现了一个新的反盗版措施，其最新的游戏，今年秋天，以防止游戏被打了一个Sky3DS。这很可能是所有即将到来的第一方游戏有新的AP（它看起来像第三方游戏都会有它）。然而，所有今年秋天之前发布的游戏仍然有Sky3DS工作，所以烧录卡就不值钱了。我会保持这个列表更新更多的游戏与AP出现。（来自谷歌翻译）
详情网站：https://www.reddit.com/r/3dshacks/comments/3uh7d3/list_of_games_that_do_not_work_with_a_sky3ds_so/

不能用老卡玩就12个游戏