If you go to
http://quiltshops.com/, you can click on any store and see which company designed that particular website - it's on the bottom on the page.
If you've done any shopping online - and if you're thinking of opening up an online shop, I would really, really hope you have. - you'll notice that the majority are very similar in the way they function. That's because they're all using the same software/designer.
So those designers are very familiar with the business, and in addition, the customers aren't required to "learn" to navigate a different system for each shop. So it works for the shop owner and buyer.
Same for
http://webstore.quiltropolis.net/- those shops use a different software. I'm not commenting on which is better, but I'm sure there are price differentials in monthly service fees and customizing.
There are some stores that have totally custom designed sites - mostly the big ones like equilter, hancocks.
The key isn't really the shop but the ease in which the consumer - moi - can find what I'm looking for - whether it's a specific fabric or a range.
You can commission the most expensive fanciest system out there. But if you input fabric descriptions like "Oriental - Blue" - you're toast.
Good luck.