Chris1964 said:
While he slightly short changes the system, if we remove titles that are ports or only exist as titles, this is the current line-up of notable 3DS third party Japanese titles:
-Beyond The Labyrinth
-Dragon Quest: Rocket Slime 3
-Resident Evil: Revelations
-Resident Evil: The Mercenaries 3D
-Dead Or Alive: Dimensions
-Kingdom Hearts: Dream, Drop, Distance
-Professor Layton vs. Phoenix Wright
-Time Travelers
-Inazuma Eleven Go
-Mega Man Legends 3
-Kagura
I think this is every notable one, though if you disagree or I missed anything, please feel free to correct me. I am admittedly excluding stuff like Pichilemon Idol Debut and Magic Pen, but I don't think anyone is really looking forward to those.
Edit:
If we're counting Nintendo, then yes, there are a lot more notable ones.