Each game needs to have a custom profile created to render in 3D. From the linked article:
3dSen is an emulator that lets you play 2D NES games in 3D. Its programmers have to create a custom profile for it to work its magic on each game, which means there are currently 100 supported games, including Contra, Super Mario Bros, Batman, Castlevania, Bubble Bobble, and Gradius.