Picking my colors comes last- I usually design in black and white first to make sure there is a strong layout and contrast, then I add color. I always use my target audience as the strongest influence in my decision: time period, mood, tone, etc. I typically look at multiple versions/colors side by side to determine which is the strongest. My go to site is Kuler which also has an app where you can take pictures with your phone or upload to the site and pull colors from it- that's been helpful at times.
Jen- to your point that Kuler only gives you RGB/hexadecimal: there is a site (rgbto) that will convert those to pantone.