Blending the Background
The most fundamental issue you have to tackle is that of breaking up the outline of your advertisement. Camouflage experts know that it is the outline of the human form, not the color of the human form, that most gives you away. This is why army snipers wear suits (called gilly suits) that enable them to stick bits of local vegetation on themselves and otherwise break up their form, it is also why we see images in cloud shapes if the cloud outline matches something we recognize. So what you must do is break up the form of your advertisement. Any block of color or text that is the common dimensions of an ad, such as 728x90 or 160x600, will be seen as an advertisement and visually ignored by many visitors.
As such what you want to do is the same as what is done on this site. You want to have the ad background and ad border be the same color, you also want that color to match the background of the space on the page where they will be located. All of this is easy to do when setting up your advertisements. This way your advertisement does not carry the shape or outline of a traditional advertisement and it is harder for users to just visually ignore it.
Do Not Trump Your Logo
Another mistake people make is putting a PPC advertisement up above their logo or header image. This is attractive to do because it is generally outside of your design and is an easy implementation to make. The problem is that people generally start reading at your logo, anything above your logo is taken to be an advertisement or unimportant, and it isn't likely to be read. If the ads aren't read, they will not be clicked on.
It is okay to put a CPM based advertisement (traditional graphical banner) where you're getting paid by views, not clicks, in such a position, but always try to put CPC based ads such as from contextual ad networks below your logo.
In this image you will see an example of a proper placement with CPM ads above the logo/header and CPC ads nestled below it.
Incorporate As Many Ads As Possible
Google Adsense allows 3 ad units per page and one link unit per page. Yahoo Publisher Network allows 4 ad units per page. If you are not using as many units as you can you are leaving money on the table.
It is important that you do not crowd your site with advertisements as it does not always work as well as you would like. Crowding ads together can actually lower your performance, so keep them spread out. This is easy if your site tends to have longer pages. An ad at the top, an ad at the bottom, and one on the side is 3, fairly easy to accomplish. If your site gets very long you can try one ad at the top, one a third of the way down, one two thirds of the way down, and one at the bottom.
The ads on the bottom might only earn a fraction of the ads at the top, but that is money and with enough traffic that can be substantial money. Also, because of the distance from the top to the bottom of most sites, you can use this many units and yet rarely will there be more than one or two ads on a user's screen at the same time.