EmuNations

Hades is a recent entry in the GBA emulation, but it has a decent accuracy, speed and features. That said, while it does not have the most features in its category, it still covers the most practical as-in game controller support...

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Fceux is an open-source Nintendo Entertainment System and Family Computer Disk System emulator. It's a merger of various forks of FCE Ultra. While not being cycle-accurate, it's has quite an accurate emulation and offers extensive tools for debugging, rom-hacking...