My intuition is that qaulia will be to cognitive/computer science what blackbody radiation and the Michelson-Morely experiment were to physics. They fundamentally violate everything we think we know about the universe. We don't even have any particularly good way of describing what we mean by things like "self-awareness" and "subjective-experience."
I believe that qualia are inherent to every computational process, regardless of the substrate. There's no evolutionary necessity that we be have a subjective nature, but it's an inescapable corollary of our evolved intelligence.
-matt