*.nds files are the basic DS binaries that most users put on their devices and launch.
*.ds.gba files have a special header attached to the front of the file so that they can be burned to old-school GBA flash carts and launched.
*.sc.nds files are actually *.ds.gba files that are renamed for Supercard users so that the Supercard will launch it in DS mode. For some reason, the Supercard launches files better when they're in *.ds.gba format, so people just copy and rename them for convenience.
You only need to have one on your device at a time.
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