claaarky - 10:25 pm on May 17, 2012 (gmt 0)
I don't think the -domain.com thing has anything specifically to do with Penguin.
To me this is more of a general diagnostic tool. It seems to indicate how much impact other sites have on your rankings and if that impact is significant then I would say it's a strong indication Google sees your page as very similar, but weaker in some way.
Then you can start figuring out why. It could just be a duplicate content or domain authority issue. Solve that and you could flip positions with the site holding you down.
It would be interesting to know if any sites seeing higher rankings when using -amazon.com or ebay are affiliates of Amazon or Ebay.