OK, I'm a shopping cart whore...
-CS Cart has a thousand times more options and overall good functionality, but runs a bit slow and they don't offer a "hosted" version. A virus infected our software and it was such a pain to re install with all our modifications, we decided to move to a hosted software. I think shop script should take note of CS Cart's features as there really are nice features on the cart.
-Core Commerce offers a hosted website with "bells and whistles" but the basic functionality of the website is buggy and half the time customers can't purchase from the website with the features that are offered. So you end up paying a lot more for...?
-Shopfactory looks good, acts fairly well, but in the end, you still have to pay them for the "back-end support" AND host it yourself. I like the software, now we just use it to produce web pages without shopping cart function.
There's others not worth mentioning...

Honestly if paypal or google were all our customers used then we would set up "buttons", but webasyst offers a nice alternative with the widgets... very smart
Complaint so far is Shop scripts import functionality is primitive or maybe just needs tweaking... as it has a hard to importing its own products correctly.