What's the difference between the two, aside from the one is paid while the other one is free? Which one works best for affiliates? Thanks.
An aStore is something you can throw together fast, using a wizard, to promote Amazon products. You can embed this site in a web site using an Iframe and it looks like you are hosting it within your website.
I have read about this issue before... An aStore you use wrapper or Iframe in your website... wrapper if indexed by google will a lot of outbound link that will be affecting google (SERPs) and google Page Rank. Webstore, (I use Apf) can blend the amazon product with your web without a lot of outbound link and i think this will better for Page Rank, even you have to work extra for this. That's why I choose Webstore...
Google often ignore a-Stores, so it isn`t easy to get them seen in the Search Engine. Either embed one in your own site, or forget it. Stand alones rarely work.