Great question! I was looking to build on to a new site and wondering whether it would be hit by one of my sites that was hit by Panda.
Background: I had some data to review on two of my other sites. Both were hit by Panda 1.0 (-40% and -65% Referrals). I found a lot of useless user generated content on both sites. When looked as a whole, they accounted for rough 50% of the total pages on those sites. I removed all those pages about 2 months ago and still no change. No Panda 2 or 3 changes since.
I have a subdomain that I use for premium content for each of those sites. There was 0% Google referral change post Panada on both of those sites. In fact the referral numbers for March and April are an exact replica of one year prior. 1 site sees 10,000 Google referrals a month. The other sees 7,900 G referrals monthly.
So in my case, subdomains were not affected at all by root domains that were Pandalized.