We have developed our own congo (multi-site) based shopping cart (CongoCart) from scratch that offers:

• Unlimited Stores with each store having unlimited users.
  Allows you to have users to process orders and users to update products.
• Combined Shopping Cart for all Stores.
  Your customers only pay once!
• The cart automatically pays all stores their portion of any orders -- automatically.
• Complete Paypal Integration.
• Users can only edit the stores they are assigned to.
• Easy to use Security System, You decided what each user of your store can do.
• Customer Shipment Tracking - Customers can login and check the status of there order at any time.
• Fund Distribution System. You can automatically take a percent of all orders for any type of fund you want (Like Advertising).
• Integrated Discount system. Give Site wide, store wide or product discounts.
• Many options for each products, to allow you to customize price, availability, shipping and more.
• Individual Tax Rates per Store.
• Complete Templating System.
  We make the Congo look like you want it.
• Each store can have a very flexable about pages.
• Complete Image Management, including automatic image resizing.
• Ability to have random product picture show up if you have more than one picture for a product.
• Complete Administration System
• Receipts -- You can print them for your records.
• Stock in carts from Un-completed orders is returned to stock!
• Easy to manage Shipping system.
• By Category, All Stores, and/or by each Store shopping.
• Themes system
• Featured Store System
• Statistics
• Live / Preview Settings on Products (With Auto-Switch at certain times)
• Searching *
• Automatically generated Contact Form based -- No more spam from web harvested emails addressed!
• Random Ordering of all products shown
• Custom Category Order
• Unlimited Galleries Per Store
• Per-Product Optional Automatic Disabling of products sold-out.
• Per-Product Optional Automatic Enabling at set date/time of products.
• Unlimited Products, Auctions, Galleries, and Images.
• Excellent Support with New functions being added all the time.
• We take seriously any and all features you request.
• VERY Low COST Hosting of the Congo Cart on fast servers
• Email to/from using your Domain Name, so each of your stores in your can have store@yourdomain.com