walkman - 2:21 pm on Feb 26, 2011 (gmt 0)
Interesting: searching for 2 affected sites site:example.com not showing homepage at first result, like was before. For competitor sites who are not affected shows homepage at first result.
Let's make sure of this: You search for site:example.com and the first page listed is not www.example.com but www.example.com/other-page.html ? Do you rank for your 'example' (domain keyword) ? Do you have a fresh cache?
Long time ago there was a penalty, link related, where the first page would be demoted and by extension everything else too.