In your theme.tpl, add a link to a css file. Call it colours.css for example and put in all the colours and formating for h1, h2, p, em, strong, a, etc, etc. I also like to do a second file which I usually call standard.css to include all the phpwebsite propritary stuff like .header, .smalltext, etc.

While developing templates, I can for example make those legacy-formatting have a red border so I can find them and get rid of them easily. No presentation code in content, neither invent your own codes ("heading"), where there already are html-standard codes ("h1", "h2", etc.) or they simply aren't useful ("smalltext").

Why the heck do I separate layout from colours and formatting? Am I being pedantic or what?

Not exactly. In fact, it's a time saver. Just copy the colours and formating of a theme to a new directory, add a new layout and off you go, basically. While defining textsizes is very important for a consistent look, it's pretty much the same steps all the time.

Your colours will stay the same for a certain theme as well, no matter what platform you are on or what device is used. They should at least, you wouldn't want to endager your corporate identity.