So I can recall that Matt Cutts has said in the past that often Google can determine if something is an ad such as a banner through their algorithm and will not have those links pass pagerank.
So let's suppose I make image called advertisement1.gif with a title and alt tag called "advertisement 1". Would that be enough of a declaration to google that this is an advertisement without having to add the "no follow" tag?
The reason for this is I know I could get more for the ads if this strategy was permitted.
You can first send the user's click to a script that then redirects to the advertiser. This is something a lot of sites do to verify how much traffic they are actually sending to each advertiser.
In addition to implementing the script, you would disallow crawling of the script's directory. Important note: have the disallow rule in place a few days before you change any links. In other words, make sure googlebot gets the new robots.txt first, or else it may get the scripts and analyze them anyway.
It's not rocket science. Google first identifies an ad section on your site and then does not trust any link within that section. If you have links without nofollow in that section they count against you.
Identifying ad sections is relatively easy, especially if it's from a known service, but even if you write the ads yourself and rotate them that *section* of your page repeats on other pages ... and what repeats is of no value.