The current theming support is half-baked. It's really only supported in the editor. Using a dark background in the editor means some of your foreground color choices don't display well (or even visibly) in some tool windows and consoles.
What I would _like_ is the ability to control the color scheme for the entire IDE. Right now, that's not possible. Someone opened these issues - WI-682, WI-2395 - but the response from IntelliJ was it's too much work. If you use a dark background for your code and wish you could alter the color scheme for the entire IDE to mute it down, ala Netbeans, vote these items up.