Bike Rider DX was one of the most popular games on the Japanese eShop, featuring a very simple runner-like concept. It's only OK, but its sequel, Bike Rider DX2 Galaxy, packs a bunch of unexpected twists, and is both an amazingly fun experience and a masterclass in level design. It's also one of the best deals on the eShop at a measly $3 (in North America, at least). It is one of the most overlooked games on the system, which is a shame, as it is also one of the best.
Pocket Card Jockey, developed by Game Freak (as in the Pokemon developer), is digital crack. Once you take a hit, you're addicted, almost guaranteed. It retails for $7 but is worth three times as much. If you're unsure, download the free demo and try it out.
Do not overlook M2's Sega 3D Classics, such as Space Harrier, Galaxy Force II, and Out Run. You could also consider the Sega 3D Classics Collection retail package, which collects quite a few of them (including Power Drift, which is exclusive to that package).
There are many others, quite a few of which have already been mentioned. 3DS, having a very mature library, and having been the leading platform in Japan for several years, is full of great niche games...as was the DS, whose own library is almost 100% compatible. Enjoy.
The best are Find Mii 2, Monster Manor, Mii Force, and if you're a collect-a-holic, Flower Town. Unfortunately, since the number of people carrying 3DS consoles around has practically fallen off a cliff, I can't recommend them anymore...making progress in any of them is going to be very difficult going forward.
