They've already made it much more difficult to bulk generate the type of links that have worked so well for so long and are pretty much standard in the industry. If you see slow adoption of your program among a broad base of affiliates that could be why.
Aside from that. Payouts are important as is the site conversion. I'd suggest you have at least 2 different 468*60 banners and some other ones. Those are mostly for decoration on affiliate sites, it is likely to be the text links that affiliates tailor to their sites that really drive sales.
Make it possible to create an affiliate link to your site in as many different ways as possible - different products, different sort orders, different search criteria, etc. Currently CJ support this for merchants who enable the capability and it is often used in affiliate sites as well as for specific links for PPC search campaigns. Again, it's not clear how the planned changes at CJ will affect this stuff, especially when it comes to paid sarch if you choose to permit that in your affiliate program.
Welcome to the wild and cazy world of affiliate marketing. :)
[edited by: skibum at 6:15 am (utc) on July 10, 2006]