Robert_Charlton - 5:17 am on Nov 2, 2012 (gmt 0)
gyppo, to take a stab at what you might be seeing, possibly it's not a question (from Google's perspective) of commercial intent vs non-commercial intent, but just the way you built and optimized your pages.
It sounds to me like you might have stuffed keywords in an unnatural fashion onto pages you wanted to rank, perhaps without much regard to the quality of the content. Commercial intent was probably why you did it, but, as tedster suggests, excessive keyword density is what Google sees.
I don't think it's simply the percentage of commercial pages that would trigger Panda. I've worked on sites where essentially all the pages had commercial intent, including small focused sites as well as large ones, and they've done just fine. It's more a question about whether the content is helpful and the quality of inbound links to the site is good.
I should add that it's also likely that your commercial phrases are more competitive than your non-commercial phrases, so pages targeting commercial phrases would be more volatile under any circumstances.