A: NO, John says if they have a NoFollow then Google does NOT use them for their algorithms.
My Thoughts: This is a pretty definitive response from John however, if links to your site comprised only of DoFollow then that could be an issue. So having NoFollow links are still important.
A: Only if you have a Manual Penalty, if it is just an algorithmic issue then there is no need.
My Thoughts: This makes it clear that it is important to have a disavow file on a site without a Manual Penalty if you have large amounts of unnatural links.
A: Sometimes it can take a few hours or a day to process the disavow file, but it takes much longer for a webspam team member to review your Reconsideration Request so you can just submit a Reconsideration Request right away.
My Thoughts: Now we need to clarify what john means by Process? As he has mentioned many times it can take weeks, months maybe even a year or more for the disavow file to be crawled. Not a mere few hours as just said.
A: John says it is because in many cases all the links you had before that were using spam techniques are now removed and in many cases were responsible for the high SERPS ranks you once had.
My Thoughts: NOT entirely true, John answered the question here, I do not understand why John and others are so hesitant to bring up the most important fact. YOU WILL NOT RECOVER UNTIL THERE IS A PENGUIN REFRESH.
A: NO, if you have had a manual action revoked on your site there is no bad history attached to your site, it is not harder to rank compared to anyone else.
My Thoughts: Repeat offenders are the only ones at risk of not recovering, however the issue of a Penguin Refresh needed to recover from a Manual Penalty is still not addressed here.
A: John does not answer the question directly, but suggests there would be no harm in using the disavow file.
My Thoughts: It seems that everyone skirts around the issue that links can affect your site in a negative way on SERPS even if you do not get a pnealty as a result. This brings up the question of negative SEO again.
A: NO, they are there only for your own reference.
My Thoughts: They may also be used by the webspam team if they are manually looking at the file and also by others in the webmaster help forums who are trying to help you.
A: NO, Google is nota ble to see this.
My Thoughts: It was thought by many that this was a possibility but John confirms that it is not.
A: Penguin is generally a sitewide algorithm, so it would not effect specific keywords or pages on a site. If you are seeing something like that then it is likely related to some other algorithmic quality issue.
My Thoughts: This is a nice bit of information to better understand and diagnose any issue your site might be having.
A: No, you should keep them if they are natural.
My Thoughts: The real question being asked here was are links that get clicked more valuable for SERPS than ones that are not?
A: Yes, the algorithm will determin what the best page to show is and there are no duplicate penalties.
My Thoughts: John goes on to mention something very interesting, he states that a page that is noindexed will still pass pagerank, so any links pointing to a noindexed page will still pass PR and other benefits through the site.
A: For Panda, YES you can if you redirect to a page with high quality content. For Penguin, NO you will simply be redirecting the bad links as well. But you could remove the page from the site.
My Thoughts: For Penguin you must clean up the issues or it will simply follow you around.
A: Yes, you can do this by putting the content you do not want crawled in an iframe and blocking it in your robots.txt file
My Thoughts: Seems to me that this could be used to manipulate Googlebot in some way.
A: No, they will be used directly by the webspam team, there are too many reason why sites will not remove links.
My Thoughts: It may help Google identify sites that are poor quality however.
A: Yes, the webspam team want to see a significant effort taken to resolve the problem.
My Thoughts: It has been reported that google wants to see around 70% of the bad links removed. I think it is more of a case of showing that you have contacted everyone and displaying if you have got a response or not. In many cases it is simply not possible to remove that many links.