Generally, I put the ads in the first screenful of the page (somewhere in the part of the page people see first when the page loads, usually near the top), and along the right border of the page (because people have their cursor near there to scroll up and down), and also along the bottom of the page where people usually end up.
The center and left areas are for content and other links. This is my opinion only but think it makes for a good look too.
As for colors, I like to blend the background of the ads into the color of my page, so that they don't show as a box. But I know other people also like the ads to be a different color so that they stand out.
My CTR's are variable, from under 10% up to 100% on different sites. It usually is fairly constant though, a low CTR page will usually stay low no matter what i do, and a high CTR page will stay high. I think it has to do with a combination of things, including ad placement but also subject matter, and also maybe what people are expecting to find when they visit the page. If they expect to find information and not buy anything, they are probably less likely to click on an ad. But it's mostly a mystery to me.