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The biggest ( and not necesarily the best) networks are cj, linkshare and perhaps shareasale is getting up there also.
I'm biased, since I manage a program at ShareASale, and I've had some very, very unpleasant experiences with both LinkShare and Commission Junction over the past 7 years.
However, depending on the topic of your web site, you simply need to identify the MERCHANTS whose products are likely to perform best on your site. (I despise CJ, but one merchant has steadfastly stuck with them, and I earn $60 to $100 per month from that merchant -- money I'd simply lose if I'd stuck with my earlier decision to "never do business at CJ."
Don't overlook "direct" or "independent" affiliate programs run by merchants themselves. Amazon is right on top of that list, but there are dozens of others who've sent me checks over the years. Many use MyAP and participate in the Kolimbo "network" (which really isn't a network, but provides many of the same benefits). I collect more money from EACH of several "indies" each quarter than from all network programs combined, but I think that's a function of my history (10+ years) more than the strengths of the merchants or programs.
If you are going to be driving organic traffic to targeted keyword filling sites then you may be better off going straight to a company with a large network to deal with them. You'll eventually get a much better payout than you ever could by going through a network. My company, <edited>, definitely takes care of our good in-house affiliates.
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[edited by: tedster at 7:55 pm (utc) on Sep. 14, 2006]
One thing I'd have to say though, regardless of which network, there are some AMs around who have a healthy, loyal following among "capable" affiliates, and not only could they suggest the best network for a given merchant, but get one started with some high producing partners going out the gate.
Added:
I think I might be a little confused. Are you a merchant looking to set up an affiliate program, or an affiliate looking for merchants to sign up with?
[edited by: Marcia at 12:23 pm (utc) on Sep. 16, 2006]