Ok its been here a while, but its only just now I'm getting involved.
I build SME websites and try to avoid e-commerce like a plague, unfortunately the internet rather than a bastion of free information seems to have become a over sized shopping mall with no floor plan.
As such commerce seems unavoidable.
If your going to build a commerce site online there is a dazzling array to Choose from of of teh shelf products. A list can be found on Wikipedia of the open source ones (probably of the others too but that's your choice).
Magento, Zen cart, oscommerce, ubbercart are the most popular from the list and ones I have experiance with. Then you have integrated products such as ubbercart drupal and wp-ecommerce. These are what I want to discuss.
If you want a totally customisable experience with a shopping cart, I'd advocate drupal ubbercart plugin. You start with a drupal install design your site and layout then plugin ubbercart, CCK and Views and develop the look and feel you desire. This is not the easy option this is the option that gets you what you want to the extreme you can with the right skill set control every look and feel, but have a production level back end management system with an excellent UI.
If you don't have the design skills wordpress and wp-ecommerce can be a excellent set, wordpress theme repositary provides some very fluid and good looking theme sand the commercial set are priced well and robust. Build your look and feel and then ecommerce bolts the shop in and holds the look and feel. Again not the easiest choice you still need to know whats going on with wordpress but you can get some dramatic results with a little work.
I'm going to work through a Wordpress ecommerce install this winter, I will attempt to provide ongoing feedback from the process.
