Google's John Mueller strongly recommended that those who are hit with a manual penalty should not wait for the penalty to expire. Instead, they should work to resolve why they've been penalized in the first place and then submit a reconsideration request.
This advice comes from the Google Webmaster Help thread that had the same topic of directories charging link removal fees.
As many of you know, manual penalties expire over a certain period of time. So do nothing and wait might seem like an option but is it?
(1) It might take six or more months for the penalty to expire. So waiting six months is often not an option for most online businesses.
(2) After the penalty expires, it doesn't mean you won't be penalized again. This site sells links and that is a manual penalty. The penalty expires every now and then and shortly after the site is penalized again. Don't do what I do.
Here is what John from Google had to say:
If your site receives a notification of web-spam or manual action in Webmaster Tools, then that will be due to a web-spam review and manual action that has been taken. While manual actions will expire at some point, I would strongly not recommend sweeping them under the carpet and hoping that they go away on their own -- at least if you're interested in having your site be optimally represented in our search results. Even when a manual action expires (which might take quite some time), if the reason for the original manual action is still relevant, it's always possible that the manual action is returned later on. In my opinion, if you're aware of issues that are negatively affecting your site's performance in search, and if its performance there is important to you, then resolving those issues is often a good use of time.
Forum discussion at Google Webmaster Help.
