Rand Fish has a very helpful article about “How to Handle a Google Penalty” and many other issues in an interview with Matt Cutts.

If your website has been penalized by Google, here are tips to help you:

• Confirm whether your website has really been penalized or whether it has only dropped in ranks
• Check whether your site is still indexed (site:url.com).
• If the answer is no that means, The site is most usually banned. Confirm from Webmaster Central after which submit a re-inclusion report after the spam has been removed.
• If the answer is Yes, then go to the next step

Does your Site Still rank for its domain name(or other unique branded names)?

• If the answer is no: You are probably suffering from a penalty for manipulative linking activity or on-site spam (Cloaking, KW Stuffing etc). First, remove all potentially bad outbound links , drop any paid link campaigns (that Google has discovered) and get rid of your on-page issues. Then, go into Webmaster Central, verify and re-submit a re-inclusion request, own up to your spam and promise not to misbehave.
• If the answer is Yes, then head to the next question

When You search for 5-6 relatively unique terms in the title tag of your pages, Does your site still rank in the top 10-20 results?

• If the answer is NO: You've most likely had many of your links wiped of their value. Google's Spam team Ids and eliminates the link love passing ability of many sites & networks every day, so you're not alone. Then, go into Webmaster Central, verify and re-submit a re-inclusion request, own up to your spam and promise not to misbehave. Go get lots of great, high quality, natural links to help your ranking improve again.
• If the answer is yes: You don't have a penalty, you've only lost some rankings. Get more quality, Non-manipulative links and review your on-page SEO efforts.

An example to understand this better is through a “quick example from someone in the RealEstateWebmasters.com forum's thread:

• We'll start with Hgrealtor's site called oaklandhomespecialist.
• The site's still indexed – it has 94 pages in Google
• It ranks #1 on a search for the brand name – oaklandhomespecialist – that tells me we're not dealing with a "sandbox"-like effect
• It's ranking #67 on a search of the home page's full title tag – Oakland Real Estate | Oakland California Homes for Sale | Realtor – that's definitely a bad sign
• On the plus side, they rank #7 for – crocker highlands homes – so they're not as badly buried as others I've seen
• And, they're #3 for temescal homes.

  This leads me to believe that while they might have had some of their links de-valued, the site isn't in grave danger, or even necessarily in need of a re-inclusion request”.

  Read the article/interview for a bigger understanding.

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