There are a lot of choices out there for eCommerce... You can go turn-key but obviously this costs more $
Hosted solutions are plentiful. Check out osCommerce and Zen-Cart for two popular ones. THey usually have supporting hosting vendors who will do all the install for you. You just upload the product.
Then there's the DIY model, can be done for around $200/year.
My company (
PRS ) specializes in eCommerce. Most of my customers have 20,000-80,000 items. I'd be happy to chat with him/you if you drop me a line off-list.