Again, see Alan Ross's "Selective Masking" techniques. Step by step how-to for pencil shading mylar (he uses Dura-Lar), how to make a DIY carrier for this stuff etc. He uses these techniques to help him print all the authorized Ansel Adams reproduction prints.
The basic techniques are non-digital so perfectly ok for discussion here (pencil shading etc.). He then moves on to the digital transparency methods raised by OP.