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PKSM is a save manager for Gen 3-7 Pokemon games. (Gen 3 games can be installed to the 3DS's internal memory like Virtual Console games, but you can't use the normal multiplayer features.) You can use it to generate/modify/clone Pokemon, but you can also just use it like an offline version of Pokemon Bank. It lets you move Pokemon around freely between games, well beyond the scope of official tools. There's a wiki link somewhere on that Github page that'll do a better job of explaining the features than me.
NOTE:
The number of mentions on this list indicates mentions on common posts plus user suggested alternatives.
Hence, a higher number means a more popular project.