Limit yourself to 2 - 3 banner advertisements per page. Always put at least one above-the-fold, meaning viewable upon loading without having to use the scrollbar. Be creative with placements in places that users will focus their eyes automatically, and blend them as much into your layout as possible.
Here's a test that I do all the time to work on site usability and ad placement. Load your site on your monitor fullscreen. Then, step a few feet away from your monitor (just far enough that you can still read the headings but not the text body). Close your eyes for about 30 seconds. Open your eyes and quickly look at your site. Recall he first few site elements that you focused your eyes on. Those locations should be where you have your calls-to-action (the page elements you want users to ultimately go to, such as a 'purchase' or 'subscribe'), and the advertisements that you want users to click on to make your advertisers happy.
Cscgal, that's really good points, also from user perspective I will suggest to place more important ads on the right side of viewers and left side of the pages as usually viewers look through more on right side, I may be wrong though on this assumption. -)