Boss encounters against yourself. Not a clone, body-switcher, or doppelgänger mimicking you, LITERALLY you

Kid Icarus: Uprising, Pit’s Body - Pit gets his soul sealed in the Ring of Chaos and while in control of Magnus’ body has to fight his own soulless body to subdue it so Magnus can put the ring on it’s hands and transfer Pit’s soul back into his body.

Fallout: New Vegas, Courier’s Brain - It’s not really a fight, but still a pretty significant encounter where you need to pass some skill checks to convince your own brain to agree to being put back in your body.