Shortest scheduled flight by an IATA registered airline is in the Kabwum Valley region of the Huon Peninsula in Papua New Guinea by North Coast Aviation. From one one-way strip (Indagen, 400m ish long at 4000 ft) to another at right angles across the valley (forgotten the name, need to dig up the old logbooks, 400 m ish long at 4200 ft) took about 25 seconds in an Islander.
Great post here, from 2003:
http://www.pprune.org/forums/showthread.php?t=90595