Finding the best ecommerce solution can be a very daunting task.  You literally can spend hour researching the different ecommerce solutions only to walk away feeling even more lost. 

Start with a check list.  One list of of non-negotiable features and a list of features you would like.  Just to give you a starting place, here is a partial list I would use.

Non-negotiable Ecommerce Features

• Search Engine Friendly (SEO) Links
• Batch Printing (able to print off a collection of packing slips with one click)
• Coupons and Gift Cards
• Shipping calculated based on price/weight/shipping location
• Importing / Exporting Products (including variants)
• PayPal Integration
• Google Checkout Integration
• Customer Reviews
• Flexible Themes / Custom Changes
• Email Alerts
• Batching of Tracking Numbers / Order Status Updates

Ecommerce Features I Would Like

• Barcodes on packing slips
• Flexible/Modifiable Product Attributes
• Basic Content Management System (CMS) integrated in with ecommerce platform 
• Auto resizing of product images

When looking at solutions, focus on your non-negotiable list and try to weed out the solutions.  Intead of farting around and looking at screen shots, demos, etc. go right to the features list and starting making sure they have everything on your non-negotiable list. As soon as you find a feature they do not have, make a note of it and move on. Don’t waste another second looking at a solution that is not right for you and your company.

Good luck!