CPA networks have flooded the Internet landscape over the last couple of years, the most popular being Adsense, BlogAds, and Chitika. These networks focus on bringing high levels of traffic to a site for a particular offer and do not rely on relationship marketing.
Affiliate Marketing is relationship marketing at its finest. Building relationships with your customers is key in trying to earn money by sending leads and sales to merchants you represent. Affiliate Networks rely on building their brand and their image through the relationships they create online.
CPA networks aim at short term verticals in niches, whereas Affiliate Networks aim for a long-term investment in their affiliates. CPA networks do not threaten traditional Affiliate Networks mainly because CPA networks offer different ads and offers than Affiliate Networks. I feel it is a good possibility that we will see some of the CPA networks team up with Affiliate Networks.
I personally prefer Affiliate Networks over CPA networks because I can choose the partners I want to work with and that I feel work best with my sites. CPA networks are becoming smarter with their Ad selections, but it is still far from perfect. I also feel that CPA networks can often feel to pushy, whereas Affiliate Marketing allows you to better integrate your merchants in to your site offering a pre-sell, specific deals, etc. Affiliate Marketing is also a more interesting field in my opinion and it is more challenging. CPA networks are nearly completely automated. I would rather be challenged by Affiliate Marketing than to run on auto-pilot with CPA networks.