The first job with the windows was to get the old "glass" out. I originally used patterned lighting diffuser for the windows, and glued it in with clear bathroom adhesive. This stuff dries clear to a rubbery consistency, and was fairly easy to remove with a palette knife (although I broke all but one of the acrylic panes - no great loss a $5 for a 2'x4' diffuser). I then had to scrape the remainder off the window frames so the new panes would fit properly.
Following some recommendations from PurpleBlancmange on the TARDIS Builer's Forum site, I mixed up some artists acrylic paint from a tube with some Isoproyl Alcohol in a squirt bottle and applied this to some new hammered-look glass.
The mixture worked pretty well on the hammered glass, but I found flat black spray paint worked well on the acrylic flat glass, so I used both for a more interesting effect.
I made the non-hammered acrylic 'glass' opaque by sanding it on the inside with an orbital sander and 100-grit paper. This allows the glass to be opaque, but still shiny on the outside, which has a better look. If you buy opaque acrylic sheet it tends to be roughed up on both sides, so doesn't have that nice glassy shine.