They were printed at a photo print shop, thus the very bright colors and great details. To paint over white bits on the photo paper, I used a Sakura Identi-Pen. I have tried other similar pens but this is the one I have found to stick really well to that paper.
The bases were cut with a craft paper punch, 11/16" or roughly 17mm. I cut one circle of a texture sheet -- printed at home, as the glue I use does not take well on photo paper -- and one circle of a thin EVA sheet (also known as "foamies") then glued them together.
Also thanks to Sean for making some interesting posts about miniature photography. There is not so much I can do with a point and shoot camera and improvised lighting, but I think these pictures are already better than previous ones taken with the camera flash (or without flash and some fudging in Gimp.)