There is a lot that goes into dealing with this issue.
You will need some good tools that can be found here http://www.reconsiderationrequests.net/tools/
You need to focus on dofollow links and this may come as a surprise but also links that appear missing.
Download the latest links from WMT, Ahrefs & majestic.
Combine them and use excel or "ScrapeBox DupeRemove" available from the link above to remove and duplicates.
Use "Blackhatlinks.com Free Dofollow / Nofollow Link Checker" to see if the link is dofollow / nofollow or notfound for the webmaster tools links.
Once done you can start to look at what is good and bad.
Under a manual penalty you are under review by a real person and they are meticulous, they will make you remove links you never even created and all sorts of crazy stuff.
Almost all links are bad in Googles eyes, this includes urls, brand mentions and non optimized anchor text like click here.
You need to attack it hard and remove as much as possible, because a penguin refresh only comes around every 6 months, the next will probably be in Feb or April.
Remove anything that has optimized anchor text no matter what or try to get the text changed if its an incredible link.
The most creditable links are ones where multiple sites are mentioned that include your competitors in some form of comparison on a forum, article blog etc... Almost all others are trash.
Also some directories are ok, like dmoz, yahoo dir etc...
OK I Mentioned before about missing links, you will find links in WMT where the link does not appear anymore, BUT in the case of a directory it may have moved down to page 3 or 4 when it was on page 1 or 2 when first crawled. The link is still on the site and if you see the site itself is trash, add it to the disavow.
Dont bother adding links to the disavow file, add domains.
example:
domain:xyz.com
domain:abc.com
This will ensure you capture all links on those domains regardless if the move around.
If you do not want to do this all yourself there are many tools out there, like Link Detox and rmoov.
Feel free to ask me any questions or send me some examples if you are not sure.
Its a horrible process I have had to do it myself and helped many others,all with success!