Someone posted a nice little tutorial on dyeing PCB's using Sharpies over at diystompboxes.com. After trying out a few experiments, I came up with something a little more interesting than flat solid colors.
(http://www.madbeanpedals.com/misc/swirly2.jpg)
It even works on enclosures, although without primer on it the colors are rather dull.
Anyway, it's simple, really. The way I did it was mark down a base layer with a sharpie color, then wet a rag with acetone, apply another color sharpie directly to the rag then dab the rag over the base tone on the PCB. Two or three colors is all it takes!
Here's my first attempt applied to a bum Poindexter PCB (before I tried the method above)
(http://www.madbeanpedals.com/misc/swirly.jpg)
I really like these. Any chance you took a picture of an enclosure you tried this on? I'd be really curious to see how that looks.