Around bustling areas like Ikebukuro, Shinjuku and Shibuya, one will find folks selling manga on the roadside. These are not official sellers but folks who go round the underground or dustbins hunting for good copies of the latest manga.
Many Japanese just leave manga on the train racks for others to pick up and read - usually left in good condition. At a glance of these makeshift stalls, all the magazines look brand new but are not.
Have no idea how much they charge though but should be less than the retail price.