My list - based on extensive customer polling is as follows:
- ability to integrate with paypal + any other major gateway
- ability to calculate taxes and build custom tax regions
- table rate shipping + integration with any major shipping provider
- Seamless integration with a content site (this one was a surprise to me and forced me to make changes in my thinking)
- Ability to easily add content pages in order to build a useful resource site around the ecommerce site
- Full, comprehensive statistics to determine effectiveness of marketing campaigns
Many other results came out of our survey - but the above answers (or some variation) were most commonly mentioned.