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Cutting towards the corners and then along the sides is a great way to cut a neat square or angular hole in paper. This option is fiddlier but you will keep your paper crisp and free from fold marks.
With the fate of repetitive motion injury looming due to the need to drill 1,200 holes, [bitluni] took matters into his own hands and built this nifty DIY hole punch for light-gauge sheet metal.