i think it depends on the 'mood' you want to set for your readers. a lot of the psychology behind colours and combinations will affect expectations and set the mood for users.

like something black, white and red may be more serious, violent, graphic, hardcore, dangerous, stuff like that.

while a blue, white and yellow is a little more light hearted, technology, sun, sky, open, fresh perhaps.

it will depend on your primary, secondary and highlight colours though and how you use them.

my two current favorite colour sites;

colour jack
kuler