If you build microsites and link them back to your own site for SEO purposes it is reported that google might penalise you. However, if you have an affiliate program and your affiliates build sites linking back to your main site will the same thing happen??
I think the main difference is that Google can see the sites that you are linking back from as being on the same IP and having the same whois information (assuming this is the case) and that can be viewed as trying to game the system. When a bunch of different sites, affiliates or not, are linking back to one site in a natural way, this should not have a negative effect but actually a positive effect.
May be some blogs creation will be more effective. You can create your own blogs in any free blog services and place links to your website there. These blogs will have different IP and different WHOIS Info and Google will see such links as "good links".