CainIV - 5:58 am on Jul 17, 2012 (gmt 0)
Here are points that might help as we have a bit of experience recently with clients in some of these positions.
1. If the site didn't receive an unnatural links penalty then its best to assume, initially that the website did not raise paid links flags. It's not 100%, but its the best base to start on.
2. Download your links from Google and favorite inbound links vendor and mix together in one long spreadsheet. Identify sites that link to you with low scores. It takes a long time (weeks) to get through and hand prospect 5000 links but it is well worth doing if you have a lucrative business model and have lost substantial revenue from Penguin. Good news is most people do not have 5000 links.
Email off and keep track of removals. Anything on websites that are low quality, have poor inbound links or metrics, or likely do not pass traffic should be turfed. Some sites will blur the lines, use your best intuition to make distinctions on those.
Use social signals in your evaluation.
3. Look at inbound anchor text. Variation and anchor text type is the key. Take aggregate snapshots of others in your niche, and develop and understand what makes a strong profile in terms of inbound link anchor text. Brand vs www, Exact match vs long tail.
Review the numbers again and again and know them very well. Then set your bars and go off and email out to sites to change anchors, where possible.
Look at competitors and where they list - especially in associations and memberships / local citations. Much of the time those types of websites will only list you as www or brand, and so those types of listings begin to dilute (aka 'make more natural') a strong over-optimized link profile.
4. Be sure to look at link diversity. Analyze the top 10 competitors in terms of the "link buckets" or link categories they have. Develop a quick working model - or pie charts of link category percentiles for all top ten websites - AND aggregate. Understand where you are deficient, and proceed in working those type of link angles.
Over time you will begin to see improvements in traffic. If you have over-optimized the website, then of course you must begin to de-optimize as well. Internal links seem to be a big one here. Keep internal links natural. Try to stay away from aggressively matching Title, H1 and page-names + internal links.
5. If you received a unnatural links penalty all is not lost. We just helped two new clients dig out of these penalties.
They are not easy to get out of but it is possible. Both of ours required 2 reinclusion requests.
Apart from the fantastic guides already available on the subject of reinclusion, the only thing I can add is:
a) Look for sources and patterns of links across networks - even ones you did not build - and remove
b) Remove any links on any directories that use remotely any wording such as sponsored, pagerank, links, SEO.
c) Read the Google guidelines again
d) Anything that looks remotely paid needs to be removed immediately. Sometimes the difference between appearing paid and not appearing paid is made by using an image link instead of anchor text, brand name or www.
e) Do NOT re-include too fast. Be absolutely sure all links that do not look editorial in nature are removed.
f) When you do reinclude be sure to include ALL work in the request that you have done to help remove links. Be honest - explain what happened.
In both of the cases we submitted we did not blame the links on a previous SEO. We simply mentioned links were built in the client profile and we removed them because we felt they went against the Google guidelines for linking.
Hope this helps.