I've had students ask me this, and I've found the answer. I just discovered an awesome bit on glass colour being created at the molecular level in this special from Nova: Making Stuff - Smaller.
Here is a link to the show - although I can NOT guarantee that it will work, because, I just get a message that it "will not play in my region due to licensing." Note to producers of show - on the internet - we are all citizens of the world.
Anyway - it is totally worth PVRing and watching. The segment on glass is about 2/3 of the way into the show, near as I can remember - and they get to talking about glass because they are discussing nanotechnology. The scientist being interviewed calls glass colouring from the 17th century (I may have the century wrong - I can't go back and verify it - because apparently I'm not in a region of the world allowed to see this. Annoyed much?) - anyway - he refers to colouring glass as "the first nano-technology." After two very nice pieces of film on staining glass and making glass (in the context of repairing and restoring stained glass windows for Canterbury Cathedral) - he goes on to explain that when the gold is in very small particles, instead of reflecting most of the light and looking shiny (like gold) - it absorbs a lot more blue and appears red. Furthermore - the shape of the molecules makes a difference too. The same applies with silver - and accounts for the yellow effect that we get from working silver near the clear glass and getting the yellow "fume" effect.
I hope you can manage to view it - it is always so cool to see glass being discussed intelligently on a science show.