Depends on the system. For SNES, your best option would be SNEmulDS, while for the Genesis your only option is PicoDriveDS, both of which support loading the files directly from the card. For the M3 Simply, there is currently no NES emulator that will let you browse for .nes files on your card, though NES DS is supposedly getting DLDI support sometime soon, so hopefully that will change. For GB/GBC use the latest version of Lameboy.
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