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.

And from another article:

…with the addition of the 3dSenMaker tool, community members now can handcraft 3D profiles for their favorite games.