The design on Stack Overflow is pretty good: minimal, simple, doesn't get in the way. I believe they hired it out to a 3rd party.

However, the color schemes on all the other sites, just aren't quite as good, superuser being the worst. Amazing what difference just a little bit of color makes. The logo on Superuser looks a little amateur in my opinion too, especially considering the other ones that were submitted.

Not necessarily true. He may just be prioritizing releasing new functionality and sites over improving the design for now.