I tried several methods and files are the best.
I agree with RJS: Ralph Lambrecht's binary method can't be beat. I have about 50 holders marked this way. It only takes a second to translate the code back to your notebook.
I too have 50 holders so last year I sacrificed a spare holder that was in very poor condition in order to determine the best method of cutting the notches using Ralph Lambrecht's system.
I found that the plastic flaps were too hard and brittle to be cut with all of the knives, exacto cutters, tin snips etc... that I tried. I found that Dremels generally melt the plastic and the cutter gets gummed up. I tried Dremmel abrasive wheels as well.
I tried making a jig so that I could drill tiny holes with a my drill press. This worked but the holes had to be a small distance in from the edge and were at an angle so the light wasn't reaching them properly. Before I tossed the test holder in the garbage I even tried a soldering iron but that was useless.
In the end a good quality file worked as well as anything I tried. Might take longer but does a neater job, you can clean up any rough cuts with a scapel.
One important detail: I used a small piece of wood, nearly the same thickness as the holder, under the flap to support it so that I didn't put any pressure on the hinge fabric.
When the job is finished I urge you to take all of your holders outside and blow them out with compressed air. I used a Porter Cable air compressor that powers my air tools. If you don't do this you will loose negatives due to grit stuck in the slot for the dark slide.
cheers, Terrance