Start with general lighting
Start by lighting your level for mood and visibility. Your goal with first pass lighting should be to create even lighting with a distinct tone. Consider all of this lighting to be natural or ambient. It is the light you would find in an area without any artificial light sources.

Once you've established the overall mood, you can worry about detail lighting.

Avoid big lights
Big lights often create harsh, unattractive shadows, so they should be used very deliberately. In general, you will get smoother, more even results with a grid of smaller lights.

Notes about color
In general, a colored light looks most natural and satisfying if it is predominately gray with just a touch of color. For example, instead of placing a blue light that is 0 0 200, you'll get better results with one that is 100 150 200 or 50 100 150. You might even prefer 100 120 140 for subtler hues.

Experiment with your textures in a test level to see how they respond to different hues and variations.

Group general lights
Once you've placed general lighting in an area, group the lights and name the node something logical, preferably with "light" as the base (so that all your light groups are together in the node view). Grouping lights lets you tweak color or radius settings more easily.

Contrast is key
Detail lighting should be your chief tool for creating visual contrast in your levels. Lighting that is generated by artificial sources (such as light fixtures or street lamps) generally looks most convincing if it is white or off-white, especially if the general lighting has some color to it.

I tend to rely either on 255 255 255 (white), 200 240 255 (bluish-white), or 255 240 200 (yellowish-white) for most of my detail lighting.