Are you looking to host it yourself? The first thing I suppose you need to determine who where the website will be. If you are hosting it locally, then you have more say over the web server. If you host it at a webhost, you sort of have to go with their environment.
For example, CubeCar, OS Commerce, and Zen Cart are all listed as being installable on my webhost control panel. So in theory I could click a few buttons and have them installed automatically.