The 3D port was designed to allow easy 3D. This port, dedicated only to 3D goggles, should have allowed developers to create more 3D games easily, but it was tragically under utilized. Only a tiny handful of commercially released titles used this port.
The connector should be self explanatory. While I can't say for certain what the V-Sync line is for, the R and L pins signal the left and right lenses to go opaque or clear at the right time. The 3D goggles function the same way as Famicom or Master System goggles do.
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