PCInk - 1:01 am on Feb 9, 2012 (gmt 0)
On using the site:mysite.com command in google the home page was not ranked first. Infact it was about three pages down.
That dates to pre-Panda days.
I've just tried a few big names and currently site:google.co.uk shows www.google.co.uk/AdWords as the top result.
Probably because google.co.uk doesn't have enough content compared to internal pages. I don't believe it is a penalty.