I'll give you that it looks fairly unique, but looking like one of those awful Windows 3.1 / 95 themes you might discover a relative using does not evoke "Power User" in me!
Once you log in, you won't see the yellow bar at the top (except when you are notified of something) and the "Welcome!" box on the side is gone. When that's done, I find that SuperUser has a very attractive color scheme. And I don't mind the yellow much because it's meant to get my attention and be dismissed, and not be a fixture of the overall design.
I'd prefer that all SO sites use jQuery UI theming and give us the ability to switch themes on the fly. This would also make it easy to create new themes with ThemeRoller and nominate them for inclusion.
It should use the "Hot Dog Stand" Windows 3.11 color scheme
SU's color scheme is easiest to look at (barring the baby-poo pop-up bar at the top). Soothing blues.
SF's color scheme is pretty straightforward, with burgundy and red and black...nice deep colors.
SO's color scheme wants me to peel my eyes out of their sockets and fry them with special sauce. Orange/Green? Ew! I'm staring at citrus all day!
Why not pick the tri-color scheme with each site, and stick with it, but for highlighting, accepted answers, etc. stick to the same highlight/bold/border scheme for all sites? IMHO, It's not the colors that matter, but how items are highlighted. Seeing questions with accepted answers is confusing at times - the highlight may or may not stand out depending on what site you're on, may or may not be a border, a background, etc. So confusing, I have to sit there and acclimate my thoughts as to what is going on each time I look at questions, answers, accepted answers, etc. Even the "standout" and "fade away" on each site can be a bit confusing at first - if I don't want to see a question, rather than making it faint, couldn't I just filter it out and make it all go away? The first few weeks it was "what the hell...what does that say, why is it so hard to read? Oh, it's because it matched a keyword that I don't want..."