I operate the technology for an online sporting goods store that currently has about 1000 active items and averages about 50 daily orders. We used Stone Edge for one year as we expanded from selling only on eBay to Amazon and an osCommerce store. We have numerous qualms with the software and are in the process of getting rid of it.
The major downfall is that there is no eBay inventory synchronization. It can import eBay orders but it cannot control the inventory on eBay, which makes it a bad solution. We created a custom query that sent the inventory data back to BT for listing purposes, but it was just too cumbersome.
The UI is just god awful in SE. It looks like it was made in 2001 (probably was) and has hardly been updated. The screens are not re-sizable and the view orders screen automatically takes up your whole screen, so forget about doing a side by side in Windows 7 with it. You'd be scrolling back and forth in SEOM all day.
There is also no easy way to view your outgoing orders and make bulk changes. There is no way to tell if an invoice has been printed (we opted for auto printing). We had numerous issues with orders not printing, and we would only realize this whenever the customer came and said hey where the bleep is my item, many times resulting in negative feedback.
They released Version 6 back in November, and then had to call everyone who adopted it and downgrade them back to V5.9. It was a hassle and caused even more bugs in the future.
The only good thing about Stone Edge is their support. You do pay a decent amount for a support contract, but they are persistent at fixing any issues that arise. They even edited the osCommerce integration script for us when it did not function properly.