All .nds files can potentially run on the sc rumble or m3 pro. I would of thought.
SnesDS and nesDS can produce both nds.gba files (for running from ram, primarily for gba flash carts running ds files from their flash ram) and .nds files (run from mem card, as shown in shaun66 review of ds-extreme)
SnezziDS produces .nds file (runs from mem card)
SNEmulDS produces .nds files (runs from mem card)