The emulators work best as cia, rather than homebrew as.3dsx. O3DS has it's own 'Best' emulators. I recommend Blargsnes, Gambette, quicknes, and picodrive. Blargsnes is a standalone, non retroarch emulator though. For GBA on old 3DS, it's recommended to install GBA injected cia's on sysnand via mini Pasta.