Ok, a couple things (I will post them here until we get the bug tracker set up for 1.0)
Minor:
- Why use the javascript for the admin login? Forces me to "Click" instead of hitting the enter key or tabbing to the button. Not a bug, just a bit of a nuisance.
- You left your information in the store owner area. Hope its fake so you don't get a bunch of prank calls

- You removed "Pounds" & "Ounces" from the default weight class list under the "Settings->Local" tab. Easy enough to add back but seems like it should just be default.
- You removed the "Processing" state from the default order status list. Easy enough to add back but seems like it should just be default.
- Admin menu loads initially "fully expanded". As page finishes, it then hides the menu. So initially it's in the way. Not really a bug, just another nuisance. Could probably call hide with a body onLoad instead of a separate call after the page fully loads
- Need "Check/Uncheck All" for long lists of checkboxes. Like in the coupon area when adding coupons and checking the items that it is applicable to.
- Existing product viewed data in the reports area, no easy way to clear it
Medium:
- In the Admin section, if you click the "DELETE" button without checking anything, it doesn't catch the error and throws a php error.
- Error deleting checked Geo Zones
- Error deleting checked Zones
- Error deleting checked order status (but it did work after page refresh)
- Error updating checked products when changing the parent category
- Deleting checked images gives error "assigned to 1 manufacturer". Should be "Assigned to 1 products"
- Sql error deleting checked downloads
- Updating Sort Order on shipping page applies it to ALL shipping methods on the list page, not just the one you changed
- Last shipping method doesn't show state on the list page. (May only be related to Zone Shipping)
- Edit Customer from the "Admin->Home->Customers tab" loads an empty form.
Major:
- No more install/uninstall on Payment page, makes it difficult to reset or remove modules. This is fine to disable them, but for new versions, it is no longer easy to just uninstall/reinstall to update the new fields
- No more install/uninstall on Shipment page, makes it difficult to reset or remove modules. This is fine to disable them, but for new versions, it is no longer easy to just uninstall/reinstall to update the new fields
- Insert order page under Admin "Customers->Order->Insert" shows "Page not Found"
- No more template selection (known I know)
That's enough for now. More to come.
The menu is certainly better now that it's no longer using that funky menu. It uses a proper UL/LI style listing. It's currently file-based still, but it's easily converted to a DB-based menu, making it easier to make contribs, but one thing at a time

Like that you are using alternating colors for list rows
I like the hover over ? question mark popups for help.