I recently made a small light shelving unit using 1/2" plywood for the sides and back. I used 3/8" plywood for the top, bottom and shelves. I set the drill about 3/16" short of the 1/2" set line and set the jig at 1/2". I used # 6 X1" pan head screws instead of the # 8 X 1". It worked just fine. It is not a fancy shelf, i am using it to store small boxes of screws etc..
That's pretty cool, I'm hoping they'll do a Kreg jig mini-setup one day, for the really small stuff, but it'd mean exclusive screws. Pretty sure I could build my own mini-version to work with panhead screws, might have to do a Google Sketchup plan on building a mini one day.
I suppose the easiest way to make a pocket jig for smaller material would be to fashion a sleeve to insert in the existing jig. It would take a lot of effort and know how to design and make a proper bit. A brad point bit the same diameter of the screw head beiing used would work( as long as there was a bit the proper lenght available) . There are bit depth sets that are available. The pilot hole could be drilled with an ordinary bit. The big question is: Is the end result worth all the effort?
Personally, I don't feel the need for a pocket hole jig, for 3/8'' stock.
The screw size would be like a #4---max of a #6.