Google is saying large numbers of links that are possibly one or more of the following have been identified:
This is a penalty, you will need to take action and then submit a reconsideration request.
It is very important however that you do not confuse this with an Unnatural inbound links (impacts links) warning where Google is not sure if you are behind the spammy link building.
Any search engine has a large number of ways to track down, like a detective, if you are the guilty one. If you are don't spend any time protesting your innocence, just get on with putting it right.
In general you are going to have to ask Google to reconsider your website and convince them of two things:
STEP ONE: Keep a diary from the start. When you submit your reconsideration request to Google it will look far more convincing if you explain each step you have taken and when you took it.
STEP TWO: Always keep in mind, as you resolve the issues, "How can I convince Google that this will not happen again?". So make notes of dates when you closed/deleted accounts with link swapping schemes, gave notice to your SEO company that you would no longer be using them, etc.
STEP THREE: In Google Webmaster Tools under Search Traffic -> Links to your site download all the links to your site into a spreadsheet and idenitfy the domains which are obviously spammy.
STEP THREE: Contact those domains and ask them to remove the link or links to your site.
If contact email addresses are not easy to find try sending emails to firstname.lastname@example.org, email@example.com, firstname.lastname@example.org, etc. and keep a record of the responses - e.g. did you get an automated "no such email" response or just silence.
For this stage, depending on the scale of the problem, you might find it faster to write code which sends out the emails for you.
STEP FOUR: For any domains where you have not been able to get the links removed use the disavow tool. In most cases do not spend time saying "I disavow the link on http://www.spammyplace.com/resources-list.html" but be wider. Just disavow entire sites so you are saying "I don't want to have anything to do with any links from http://www.spammyplace.com".
STEP FIVE: Once you have removed all the links that you have remember to close/delete any accounts you have that lead to the problem, such as link exchanges, link wheel schemes, etc. Document what those services were and when you closed/deleted the account for your reconsideration request.
STEP SIX: Submit your reconsideration request to Google via Google Webmaster Tools (there is a request button beside the penalty message. Make sure your request is full and includes everything that you have done and documented.
I'm Tim Hill, a Search Engine Optimisation and Online Marketing specialist. I created this site to help others understand that SEO is not a mysterious black art!.
If your a newbie try the Getting Started in SEO page, otherwise feel free to dig around and learn more.