Where on a webpage is the best chance that a visitor will notice an ad and look at it?
Best chance is always the first part of the page they look at, the header(top). Whether or not you actually want to put an ad there probably depends on the content and design of the page. A lot of the time the logo will be on the upper left and you will have some space for an ad on the upper right. Another higher place would be right below the nav. (I'm not really a huge fan of most of these spots, but if its a commercial site, why not?)
The sidebar is usually a good spot because it is out of the way of the main content and if the content is long enough, you will have plenty of room. It is also pretty common to have an ad below the intro paragraph, or first blog post, on the home page. That way users will spot it while they are reading through.
But when it comes down to it, eye tracking studies have shown that users generally ignore any banner ads. Your best bet(and probably only) is to try and really target the ads to the user. Half the ads out there just look like spam so why pay attention to it? I suggest looking into ads that directly relate to the content of your site whenever possible.
People are very good at ignoring ads where ever you put them. There have been studies done where users eye movements were tracked and they show that they hardly ever look at ads.
This study from 2007 shows this very well.
If you choose "non-standard" locations for your ads, you might find people look at them to start with, but once they get used to the layout of your page they'll start to ignore them again. You might also find that people find the non-standard locations so annoying they stop visiting your site. A couple of years ago I was working for a newspaper and they redesigned their web site to have ads all over the place and mixed in with the content and it looked terrible. I'm sure we lost visitors because of it.
So, by all means have ads, but don't make them too obtrusive. If someone's looking to buy a camera (or whatever) they'll notice a relevant ad and if they trust your site might even click it.
By now we are well trained to ignore ads, but more important we hate when websites try to force us to look at ads by using non-conventional techniques.
Since it is more important to keep your users happy in the long run place ads in non-obtrusive places in your site, like the header, the sidebar, between posts and other common places.
Notice the way facebook only puts a couple of small ads on the bottom right of the page. According to most heat-maps this is the coldest spot of the page, which is why facebook put the ads there, to keep the users happy.
Relevant, infrequent in-context text ads are much better at engaging invested readers than obvious banner ads are at desperately trying to convince disinterested, banner-blind users.
You can sprinkle text ads inside your main copy, but don't try to fool your readers. They will feel cheated and punish you for it. Jeff Atwood's does a good job of serving up text ads that are relevant to the audience on codinghorror.com.
* Shameless link.
Recently, I've been seeing ads at the bottom of the browser window (like a sticky ad). See this as an example, noting that the link may only be relevant for a narrow timeframe .
What struck me was that if I was interested in the article on the page, I noticed the ad right away because I was scanning down to the bottom. In this particular example (when I got to the page) there was a video playing without sound, but as soon as I hovered my mouse over it, the sound came on. What a very interesting feature.
I agree that after a while, I may start to ignore these ads as well, but in terms of take-away, I am seeing these a lot more than I'm seeing anything in the header or sidebars.