I oversee a number of ecommerce sites for clients, most of which are OSCommerce, Zen Cart (yea I know) and one Magento.
None of them were hit by either Panda, and some gained - even the Zen Cart sites, that don't have the user friendly URL plugin.
None of them have much in the way of linking going on, but to my mind, the technical issues are at least half the battle with an ecommerce site, and that's where I think we've made a difference.
For example, on the Magento site:
NO manufacturer descriptions whatsoever, all of them handwritten. Granted, some are pretty sparse till I get around to getting them tarted up, and some are going to be sparse by nature as they are five URLS of pretty much the same product only in a different size/dimension, but it's still our own text.
All product and category pages have UNIQUE titles and meta descriptions. Took me a slap month to do it, but I wrote every single one myself. And while some are similar, GWT reports only 4 duplicate titles (newly added products I haven't gotten to yet) and a dozen duplicate meta description tags, out of almost 10K URLs. That's not too shabby.
I currently have 55K URLs blocked by robots.txt, according to my GWT, which is five times the number of indexed URLs. Why? Because I block the search results, the pagination, the sort, and anything else that might create duplication or garbage URLs. I also block tags, admin pages, and product comparison pages. Not all my product and category pages get traffic, but I'm reasonably sure they're all indexed, and for the most part, only indexed once. I'm of the firm opinion that what you keep OUT of the search engines is just as important (if not more so) than what you let in.
I use the Canonical URL tag to keep categories out of the product URLs.
I don't want the site to look like it's running on autopilot, I want it to look like it's being cared for, by a human being (as much as I am one) and it does. I've made plenty of mistakes with it, and I'm still learning how to do things right, but I think the technical stuff is *really* important on these ecommerce sites, and I think Google pays attention to this stuff.