The ones on the side are the FX chip, which is used to produce 3d graphics on the SNES. It's almost like the 32x of the Sega Genesis, but built right into the system. Games like Starfox, Stunt Race FX, and Yoshi's island will have the prongs on the side.
Generally speaking, any SNES game that needs a coprocessor of some sort to function properly will use those pins to allow said coprocessor to interface with the main system. The Super FX is the most well-known of those coprocessors, though others exist. Coprocessor-equipped games should function on all official SNESes, and probably new clones like the FC Twin as well (though I can't confirm or deny that).
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