Am 100% sure Magento will run multi-store Ecommerce. So you can manage a lot of different shops, on unique domains, from one admin panel.
Some CMS will run it, Expression Engine is one. And Drupal like we've already mentioned.
Apart from these few you have to look to bespoke solutions.
I know the guys at Webnetism - they have a multi-store ASP.net Ecommerce and CMS system - and really nice it is too. Custom system though, and has costs associated with it at a high level.
We sometimes use a system from White Box Solutions. They have a multi-store Ecommerce system running on ASP Classic. It's not free though, cost is something like in the region of £2K just to even get the code, before you've done any mods and custom programming in there. Some of their clients run 30 stores on one admin panel. So all the orders come through to one master admin panel, and there's a flag in there that tells them which store the sales was made. It prints out unique invoices too.
The idea is that you build one master store, and then build niche stores - focussing on specific product categories. Good for SEO