I have never filed one, but two close calls spring to mind:
The first was during training, on my second solo cross country. I was descending on final approach at around 500' (private grass strip) and a Hawk flew under me, about 150' below. A few moments after seeing it, I realised I wasn't descending any longer, as I had subconsciously applied full power.
The other one I recall was about 5 minutes after climb out, at perhaps 1800' a big twin (not sure of the type, but 4/5 windows down the fuselage) descended from above me right in front of my nose, on the same heading. He was low wing, I was high wing, so it would have been difficult for either of us to see. 'Phew, that was close' I thought as I watched it fly off ahead. Just then, he started a turn back towards me. I turned right to avoid and started climbing, as he by now was lower than I was, but he turned left at the same time, and this time passed just under me.
Maybe that one would have been worth filing...