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I mean focus on removing links from homepage
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?? It's not the links ON YOUR pages, it is an obvious footprint appearing for links pointing TO your root url. Forum signatures, "bookmarking sites", article dumping sites, blog "comments" and the like all pointing to the root is in no way shape or form "natural"
One thing that you HAVE to remember is that search enginges do not index and list "pages" or "sites". They index and list
unique URLs, so looking for unnatural patterns is really not that difficult. It's simply statistical analysis.
A website that hasn't been infected by a SEO "expert" will have all kinds of links to all kinds of document URLs on the site, with smallish spike and a significanti "long tail" curve
Badly marketed sites will have a steep drop off from the median point and practically no long tail curve.
It is THIS shape (the bell curve) that Googlers mean when they talk about a "link graph", and if you draw a graph of results, patterns in data are so easy to spot.
What would I do?
First off, the genie is out of the bottle where your links are concerned and taking them down or having them changed to point to different URLs is probably out of the question. Which of course would be one of the best thing to do.
One "Googler", John Mu I believe, suggested that starting again on a new domain name would be the only way back for the severe cases, and of course all the usual suspects, who probably helped to get many into this position in the first place have come out of the woodwork offering more words of "wisdom".
So, if I was in this position, I would probably do nothing at all for a couple of weeks or so, at least until the "dust had settled" and Google are looking at "turning the knob down" a little. At that point the "least worst" offenders will be showing signs of recovery and the way forward will become clear.
However:
If I had been doing "agressive link building", the forum signature links would go, or at least NOT be "you most impotrant keywrod".
Any silly "link scheme" in whatever shape it happens to be would be gone.
if I had my own "web2.0" sillyness going on, rewording and repointing those links would be done, or them taken down.
"Article" link building would be gone, if the articles are any good and actually related to your market place put them on YOUR site.
And anything else that was done
PURELY FOR "ranking" should go.