I'm a freelance SEO consultant working in the London area and have worked on a site with the Unnatural Link Penalty (not as a result of my work - I was only engaged after the penalty was in place -which 2 other "SEO consultants" were not able to identify). Their penalty from Google has now been lifted. Based on this experience, the free tools below can help you diagnose a ranking drop on Google, potentially due to a manual Google Penguin "Unnatural Link" algorithm update penalty notified by a notice of detected unnatural links (please note that not all of Google actions on a site will be notfied via Webmaster Tools - see http://www.youtube.com/watch?v=sXaJ2u3Y9js and that the list below is to address Google ranking drops based on backlink issues rather than low quality internal site content). They are all (relatively) easy to use & can also help you with the link disavowal & reconsideration request: http://googlewebmastercentral.blogspot.co.uk/2012/10/a-new-tool-to-disavow-links.html.
I would recommend that you get a SEO expert to review your work for accuracy and completeness.
Here is a list of what Google calls 'Link schemes' (any links created with the intent to manipulate Google PageRank or a site's ranking in Google search results may be considered part of a link scheme and a violation of Google’s Webmaster Guidelines) which may result in a ranking drop, "Unnatural Link" manual penalty / algorithm update penalty or deindexation: https://support.google.com/webmasters/answer/66356?hl=en.
1. http://urlprofiler.com/blog/custom-scraper/ - get contact details in bulk for a list of URLs who have "Unnatural Links" to your site for free to help with your Reconsideration Request. It would appear that all Google wants to see is that you have asked for these links to be taken down - nothing more. It will make it easier for the sites in question if you detail where the links in question are to be found on their site but Google (it would appear at time of writing 2.9.13) doesn't require this.
2. http://www.semrush.com - see the 'Total Keywords' report in the 'Charts' Section under the Tools category for 'ballpark' approximate data r.e. total top 20 rankings of a site for phrases on google.com / co.uk etc etc over time. You can export this data or just take a screen-shot. This tool will allow you to track the position of a site for 1 key phrase for free over time too with a free account. http://feinternational.com/website-penalty-indicator/ offers a free Website Penalty Indicator tool using SEMrush organic traffic data, which should be taken only as an indication of actual organic traffic. Similarly, whilst the Google update overlay may indicate an algorithmic ‘penalty’, further verification may be required.
3. http://www.ahrefs.com - the top level report with details of site-wide links, referring domains / pages for anchor text phrases. An alternative is http://www.removeem.com/extended-preview.php?domain= which offers richer info on the linking pages e.g. MozRank. MozRank refers to Moz’s general, logarithmically scaled 10-point measure of global link authority (popularity). MozRank is very similar in purpose to the measures of static importance that are used by the search engines (e.g., Google's PageRank) but will not tell you if the site in question has a Google penalty.
4. http://www.linkdetective.com/ - analyse your (free) export of 1000 links from http://www.opensiteexplorer.org. Generate a back-link profile using semantic mark-up and URL naming conventions to group links by type (e.g. comment, article, directory etc).
5. http://www.majesticseo.com - the best back-link data on the market? Get your own site's back-links for free.
6. http://www.barracuda-digital.co.uk/panguin-tool/- see how Google's algorithm updates may have impacted your website's organic traffic in terms of visitors using the Panguin Tool, including Landing Page Visit Variance & Keyword Visit variance over time reports. This requires installing Google Analytics: www.google.com/analytics/.
7. https://www.google.com/webmasters/tools/home?hl=en - view your site's latest back-links and any notification from Google r.e. a notice of detected unnatural links to your site with Webmaster Tools. You can view the change in clicks, impressions and average rankings for the Google Web Search queries that you are ranking for pre- and post- a recent Google update (see list here: http://moz.com/google-algorithm-change) via the 'Search Queries' section (https://support.google.com/webmasters/answer/35252?hl=en). In addition, you can also see information about the pages on your site that were seen most often in search results (top pages). To specify the period for which you want to see data, use the calendar drop-downs above the graph. (By default, they'll show the last 30 days of data, and compare the daily average for the selected period with the daily average for the previous period.)
8. Using a free trial of Link Research Tool's 'Quick Backlinks' tool you can get access to a list of "bad links" (this may require review): http://www.linkresearchtools.com/videotrial/. This may help you identify the types of links you need to disavow.
9. Using the free SEO Visibility data on a domain from Searchmetrics can give you an indication of any recent issues over the last 3 months: http://suite.searchmetrics.com/en/research/domains/visibility?acc=0&url=ebay.com&cc=GB. See http://blog.searchmetrics.com/us/2012/11/14/search-metrics-moments-what-is-seo-visibility/ for an explanation of this data.
If you're not a Microsoft Excel / spreadsheet wizard (like me), the following tools can help you with the creation & updating of the Link Disavowal documentation:
In short, these should be all the tools you need unless your dealing with thousands of low quality backlinks to your site.
Please contact me if I've I missed anything important or if you have any questions.