olly - 8:40 pm on Jun 24, 2010 (gmt 0)
I wouldn't freak out and put the old site up unless it's already been 4-8 weeks.
I am inclined to agree with this. We haven't done anything dodgy and I think the best strategy is to just wait, as there are no obvious reasons for not being present in the rankings. This is confirmed by the fact that, apart from the home page, the site is healthy from a ranking perspective.
I have also debated whether or not it was the site design. The fact is they are both major events. It seems to me that the algo change has done more damage to longtail rankings or small sites. Our site is pretty well established with 600+ pages, quite a few links and an authority domain name, with only the home page having been removed. So my money is still on a penalty imposed by the site update. I could be wrong though..