A few link-building best practices, post Panda/Penguin
All the recent changes have everyone in the SEO world in an uproar. Within hours of the detection of a new algorithm release, we're bombarded with posts promising "7 Ways to Recover..." or "How to Penguin-Proof your Site". Sorry, but it's impossible to make any sort of decent judgement of what has happened to your site's rankings, much less how to recover its previous rankings, that quickly. Don't fall for every piece of link-bait advice offered, regardless of the source.
Folks tend to confuse correlation with causation too often, and particularly now, with both Penguin and Panda to consider as possible issues, that can lead you to take erroneous actions that will make your situation worse, rather than better.
The first piece of advice I would offer, is above all... take a deep breath. Think it through and analyze your situation, before doing anything. Knee-jerk reactions are NOT the order of the day!
Second, never - I repeat, NEVER, submit a reconsideration request unless your site no longer appears in the index for a vanity search (ie: http://mysite.com). The odds are great that if your site dropped several positions, it is due to dampening of the value of inbound links, rather than a "penalty". A reconsideration request (and the attending changes you might make to your links prior to its submission) simply signal to Google what additional sites they should look at as possible link-sellers/networks. Never telegraph that information, when it's avoidable (and it usually is avoidable).
One of the biggest issues we're finding with our clients is in their link profiles. Penguin seems to be heavily focused on examining links, in terms of sources, anchor text and of course, relevancy. There are some things you can do that should be helpful in recovering, and particularly in preventing future issues:
Vary your anchor text. If your widget site has 20%+ of its inbound links anchored as "blue widgets" or "red widgets", that's not "natural" in the search engine's eyes. We've found that the more diversification present in anchor text, the better, in avoiding algorithmic action. An exception to this when the anchor text is "widgets.com" or simply the link, without anchor text, such as mywidgets.com. We've seen profiles of 40%+ without anchor text, that were unaffected.
Vary your linking site types. Don't overdo the links from forums, blogs, directories or any other type of site. "Natural" linking means a wide variety. I've seen profiles that exceeded 80%+ from forum signatures on sites that got tanked. Removal of the signature links on those forums resulted in an almost immediate recovery. Spread your inbound links as much as you can, across a wide variety of site types.
Vary your target pages. Site-wide links should be few and far between. Linking to your homepage is something that should be done very sparingly. Aside from the fact that fresher, more focused content found on inner pages can be much more relevant, the algos seem to be picking up on the heavy focusing of inbound links to upper-tier pages, as well. I say "seem to be" - that's correlation, not causation. :wink:
One of the things that Google is suggesting is that if you suspect you've been hit and you have "questionable" links, you should remove them. Good luck with that. If they're on blog sites of people you know, maybe... if they're in forum signatures that you control, certainly... if they're on directories, possibly... otherwise, the chances of tracking folks down and getting them to take action are slim. We've been lobbying Google to enable a means for webmasters to report "ignore this link", so that it will be removed from the batch of ranking factors, but if or when that will happen is anyone's guess. Do what you can, and build new safe links to help dilute and diversify.
This obviously isn't a definitive list... no such thing exists, especially when things are still in a state of flux. Some sites that are guilty of blatant link-buying may seem to have escaped notice, while some innocents may suffer. It's the same with every major update, and Google is aware of this. Their post-release efforts are heavily focused on finding those things and remedying them. It helps them make the new algo better. Nobody likes it, but like the occasional hailstorm or earthquake, it's just something we have to learn to live with. ;-)
EDIT: Another point in diversifying your link profile: Don't concentrate on acquiring only links that are not nofollow. Again, this isn't "natural" in Google's sight.