After the assertiveness of my first two rules, this one might seem a bit obvious and tame. Anything but. Not every set of colours is a colour scheme, as I propose it.
So what makes a set of colours a ‘colour scheme?’
First of all, it fits. I assume you know the point of the site you’re working on—its reason for being, who the site owner wants to visit, what the site can do for them. If it’s selling something, you will have worked out the “elevator pitch.” The colour scheme has to fit in with this. (Actually, you can think about point and purpose and audience and message as you experiment with colour schemes. Finding the right colours can actually clarify the function of a site. The important thing is that they are right for one another.)
Secondly, the colours are used with absolute consistency. The same colours are used to do the same jobs, on all the pages of the site. Or, if there are variations for contrast or clarity, the variations are consistent. (In the first version, all your secondary headers would be the same colour. In the second version they could always be a different colour—but drawn from (say) similar bright hues, such as you might find in a child’s paint box. This, of course, demands greater sophistication and experience.)
Thirdly, the colours go together. You can use a colour wheel; play with the sliders for hue, saturation and brightness on your favourite design tool; pick neighbouring shades and tints from a favourite digital image; etc., etc. At the end of this play, you must have colours which complement one another. (‘Complement’ here includes appropriate contrast.) When you look at your Web pages, you must see a visual whole, with no ‘bum notes.’