idk if this is common knowledge or not but for GBA VC and DS cart games, if you hold start while booting, they go into original resolution instead of scaled.. also for GB/GBC games they do it too but also have a custom border.
This has been know for a long time, but it's the first time i heard about GBA.
And with GB and GBC, if you turn on the 3D effect while playing in original resolution, the 3DS will simulate the effect as like the originals.
NES/SNES are always running at the same resolution and 4:3 aspect ratio. However for SNES you can change the aspect ratio in settings to original to make the picture crisp. No 3D effect is available for NES/SNES games.
UGH WHYYYYYYYYY IS THIS A TUTORIAL???? THIS WORKS FOR DS MODE, GAMEBOY AND GAMEBOY COLOR! You can also turn the effect of the original Game Boy VC by holding L+R, and then press Y to toggle from Green or White Game Boy.