You may have noticed that it simply isn't enough to put some default styled ads on the top corner of your page and expect serious money out of them. Users know what ads are, they distinguish them from genuine content, and they just love to avoid them. Even if you have a very popular site, a default looking ad at the top of the page will get you pretty much nothing, or almost nothing, in the best case.

So, assuming that your site is visited enough to be a potential revenue source, your only problem is the low click through rate (CTR) of your ads. CTR is a very important term in the world of pay per clicks advertising, it enumerates the percentage of visitors who click the ads, from all visitors who see the ads. If you like to talk numbers, here is your math : CTR = (ad clicks / page views) * 100%. A pretty good CTR is around 10%, since more is simply non-natural and will most likely make your PPC agent suspicious about the validity of your clicks. I doubt however that any optimization will get you past the 10% CTR, but, I could be wrong.

In order to increase your CTR, there are a few "secrets" that you need to know about what is more "clickable" in your visitors eyes. Here are few guidelines about choosing the right palettes for your ads:

If you want your ads to produce more clicks, don't make them look like ads. Do everything you can to make your ads look more like genuine links and content. Obviously, without altering the code, adding incentives, or hiding parts of the ads. That is against the TOS of your PPC agent, and will get you banned. The detailed steps are:

1) You ads background color should be the same as your websites.
2) The ads shouldn't have any borders or special distinguishing visuals.
3) The color of the links should be the same as on the rest of your page.
4) The URL at the bottom of your ads should be the same color as the text, in order not to stand out and draw attention to itself instead of the link you want users to click on.
5) The ads plain text color should be the same as on the rest of the page.
6) If you want to get more extreme, match the font-face and font-size on your site to the font on the ads. This is likely to be unavailable as an ad customization option, so this is a change you should do to the rest of your site, instead.

After matching the visual properties of your site, your ads should be sized and placed correctly.
It may surprise you, but a banner ad (like the AdSense default) at the very top of your page, won't draw many clicks. This is because users are used for ads in this place, and will not bother to check yours out. You must place your ads in "unexpected" places.

Logging and research of many online marketers came to the next conclusions about where to put which ads:

1) The right side of the screen is much more visually attractive for the visitor (it's psychological). Thus, side ads (the tall ones, or a stack of rectangular ones) should be placed at the right of your content.
2) Ads that look like menus (the AdSense link unit for example) should obviously be placed where the user would expect a menu, or beside a real menu.
3) Putting ads in the middle of your content, is an excellent thing to do. If your ads look similar to your content (as described in the previous list), the visitor will click them much more often, as good contextual ads actually enrich your content here. Rectangular ads fit in the middle of text nicely, especially the big ones.
These guidelines can increase your CTR a few times over, however perfecting them is left to you. If you can get your hands on tools that will let you log the efficiency of your ads, use them. There is nothing like trial-and-error to see what's working better, and what should be changed.