When the Final 4 out of 5 realize they are Cylons, and Sam is about to get in his Cockpit, he says to the Chief "what if a switch flips in my head, and turns me against my own"
While hes flying around a Cylon fighter does a U turn and scans Sams eye with a bar code Scanner. You later see a a Red flash in his eye.
So my questions is what exactly did that do? i never saw any significance in later episodes, but it looks like i missed something. Did he get an Upgrade or something?