Truly a timeless thread, because there are few certainties in life, but losing your pencil, when needed most, is a definite.:p
Despite some worthy and adventurous theories, I think Carry Pine is close to the truth, that a form of gremlin runs about the workshop. For fun they move things about, like safety glasses and wing nuts, but pencils are different. I have found clusters of them tucked away in dark, inaccessible corners of the workshop, and it is my considered opinion they (the shed gremlins) are nesting. Pencils seem to be their favoured nesting material, not unlike the car gremlin, which nests in a torus of Biros (that dozen or so you "lost" in the glovebox), usually found under the back seat.
Cheers:D