What I do is small info on negative holder sleeve - for example: Nikon F3, nikkor 105/2.5, Rodinal 1+100, Efke 100, Hamburg, 2013-07-03 and negative number. Every negative has unique number (2012-1, 2012-2 ... 2013-1, 2013-2 ...) that is exactly as folder name of scanned negatives on hard disk.
And one small dot on negative holder sleeve below every frame that goes on print - so that I know which one are good ones that I printed.

I don't do contact printing because lots of my frames are under/over exposed - so it is hard and also I am saving on paper.