Color Scheme Designer is a tool I have been for a while now, but more recently I discovered Color Sphere. Both are very helpful when it comes to choosing an harmonious set of colors. Color Scheme Designer gives much more control over colors repartition and has more export options, while Color Sphere has more rules and a simpler interface. Both allow to test the color set against various kinds of color blindness.
During last year I tested and adopted two tools for my environment: the Anonymous Pro font and the Solarized color palette. After months of use, there is no way back: the difference of comfort is significant, and any text application allowing to be configured so gets them on my work stations.
Solarized has a repository of configuration files for various applications. Unfortunately those are made by different people, with different tastes, and thus the color choices are not consistent from one application to another. This means you may still have to go through a good deal of tweaking if this is annoying to you.