RKG has a great post on the variance in conversion rates across Google and Yahoo's syndicated networks, and how there's one strategy that can be used at Google at least, to help de-average and bid a bit more appropriately then using a standard configuration.
While you can't set separate bids for each source of traffic on their network individually (although you may well see this in the future), you can set a separate bid strategy for Google, and for all others grouped together.....
"One set of campaigns is set to Google-only. A carbon-copy of those campaigns is set to Google + Syndication Network. The bids for the Google-only campaign are higher because the conversion rates are higher, hence on Google.com only the Google-only campaigns are in play. That means that the Google + Syndication partner campaigns actually only serve ads on the syndication network and the bids can be depressed en masse for that traffic."
Eventually hopefully Google will let you bid separately for each site. And maybe some day add even more variables into the data set that you can bid against. One day search may even look like ad exchanges today, letting you place an bid on each individual impression.....imagine being able to bid more or less based upon someones search history, or on demographic data you may have stored on a user, or on purchase history info you may have on a user....this could get really complex at some point in the future, and really separate the serious math people from those that are kind of winging it.
Anyways, make sure you check out RKG's full post, there's some great data that's well illustrated.

@TO - RKG's post points out that these indexed price points aren't enough.
Great post JD
Posted by: Hamptonsrob | November 25, 2009 at 04:55 PM
It's a good point, but worth noting that Google addressed this several years ago. Their "smart pricing" looks at average conversion rates indexed against Google.com conversion rates and pays distribution partners less for lower quality traffic. They always maintained that they passed these discounts directly on to advertisers, meaning that there's no significant benefit of this strategy on Google.
I think the point still holds for Yahoo, though.
Posted by: Tim Ogilvie | November 24, 2009 at 03:01 PM