Hi There,
I have been having trouble with the same thing and have found some good advice throughout the process of recovering.
One method that I have heard people suggesting was to change the URL of the page that is affected and then set up a redirect to the new page. From personal experience, I can tell you that this doesn't work. It is simply a very short-term fix (i.e., a few days if your lucky), then Google will start punishing you for the redirected page.
If it is only specific pages on the website that are being affected, try to pin-point the exact aspects of those pages that could be deemed as black/grey-hat. If it is the case that some of your webpages are ranking then you can take solace in the fact that your whole website hasn't been banned. So there is still hope to recover.
Try using OSE to check out all of your different anchor text and links, as well as looking through webmaster tools. If you can, contact these websites to have your link completely removed because at the end of the day, if your not ranking because of these links then they may as well be removed completely.
You could also attempt to remove your old pages that have been punished and create new URLs completely (don't redirect the old pages, simply delete them altogether) and just use the old content that was on them. This way you will get rid of all of the links to the punished page, and start a fresh new page with your old content. Re-index the pages through Google and slowly but surely, you will eventually start ranking again. Obviously this is not possible for your homepage, so maybe use this methods for some of your other pages and then put most of your effort into sorting out the linking profile on your index page.
I hope this has helped slightly and good luck!
Matt.