The very first thing you have to do is determine if your search engine penalty is a result of a manual act or simply because of an algorithm update. For instance, the Penguin update was a change to Google’s algorithm so if your site’s organic visitor traffic dropped off on or just after April 24th, 2012, there is a good change it’s because of an algorithmic penalty. A manual penalty means someone (a human employee) at Google reviewed your site and decided to impose a penalty to your site specifically. This happened to JCPenney after their site got ousted for buying links.
Why is it important to determine if your search engine penalty was a manual action or the result of an algorithm change? Because how you go about resolving the two is very different! Sites that suffer from a manual search engine penalty can submit a reconsideration form after they’ve addressed the issue that led them to being penalized in the first place (such as buying links). A reconsideration request doesn’t guarantee an immediate recovery because a Google employee has to manually check your actions and see if your site deserves to be “un-penalized.” If you failed to properly address the real issue (let’s say you thought it was a content problem instead of paid links) then the penalty won’t be lifted.
Recovering from an algorithmic penalty can be a little trickier because it’s not as easy to pinpoint exactly where you might have gone wrong. For instance, Penguin targeted sites with poor quality link profiles, over use of exact-match anchor text and other web spam tactics. How can you be sure of what you’re guilty of? My advice to site owners that were impacted negatively by an algorithm update is to make one change at a time and then see what happens. For instance, you could start with your link portfolio. Visit each inbound link and determine whether or not it’s a valuable link, one you want associated with your site; if it’s not then add it to another list and slowly work to remove those over time (maybe 5-10 a month). At the same time, you want to start replacing those low-quality links with quality ones so as to tip the scales in your favor.
I’ve done several SEO audits for site owners over the years that are suffering from a search engine penalty and they are always in a rush to implement all the changes all at once, thinking that will help them bounce back faster. The reason you want to make one change at a time is so you can test what is and what isn’t working. If you make too many changes at once and something goes awry how will you know which change is at fault? You also can’t be sure of how the search engines are going to react to a lot of changes at once, so it’s best to work slowly back to recovery.
The hardest part about resolving an algorithmic penalty is that you have to wait. Until the search engines release an update refresh and re-crawl your site you won’t fully recover. Hopefully your efforts will help you slowly build back up your lost traffic and rankings, but don’t expect to bounce back 100% until the next algorithm update comes down the pipeline.