I am talking about something like CJ, which pay for leads/sales or something like Casale Media that pays by impressions.
Yep affiliate programs can make you a whole lot more - if you select good ones with great conversions and put them on targeted sites. If you have a VERY high traffic site with lots of generic or diverse traffic - lets say a humor site - then CPM ads can work better because that type of site with very untargeted traffic is harder to monetize through affiliate programs.
If you have a site that is very popular interms of daily impressions, woudn't CPM ads mean substantial guaranteed income, whereas the affiliate programs have to lead to sales.
CPM ads, if you have the traffic, always make more sense than CPA links. I mean, in certain circumstances, where you can make a CPA ad convert at a rate that is worthwhile, then CPA wins. But by and large, as a publisher, CPM is the way to go. You are being compensated based on eyeballs, and not on actions...the risk is all on the advertiser, not you. Now granted, if you get a terrible CTR on CPM ads, your ability to run them will be limited, as advertisers will pull em eventually...