Check out
http://www.buildpage.com shopping cart with affiliate software already built in, full accounting backend (dump it into quickbooks or peachtree)). If you need soemthing a bit more customized, email
[email protected] for a quote. His stuff is written in ColdFusion...we've been running it on NT/2000, Solaris and linux with no hiccups and it can run in unix as well. The initial price is based on per item in the shopping cart and is extremely flexible and scaleable.