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How to be sure that your website is penalized?
Penalized = site rank is lowered, all pages, SEO used on site is not acceptable
Filtered - duplicate content on website pages, could be indication of stolen content.
Banned = site cannot be found on SERP index, if it is not accidentally, you are a bad guy..
First sign is - no more visitors from that search engine. Try to enter your domain name in search box. If only a few pages appeared from your site, it could be that is red flag there.
If your site (domain name) is not listed on the first place when you are searching for your domain name, and if search engine spider visits your site often, and there is no problem with link structure (all pages visited from SE spider), that is red flag.
If you are using any of "Black Hat" methods, remove those codes from your pages. (hidden links, hidden text, page cloaking, keyword stuffing, hidden redirections...) This includes CSS cloaking too, whatever other says, I saw Google and Yahoo spiders parsing css files
Affiliate links - if your pages are overloaded with affiliate links, add more content and remove not important links. Hide links with redirections what spider cannot follow.
Link spamming - duplicated menus? Many links from link farms in a short time? Lot of content added to site in a few days?
Duplicate content - titles and descriptions on pages the same, first paragraph on all pages the same? About duplicate content filter, see below.
Shortly, if above example (domain penalized) is in question, there is something on most of your pages that is not acceptable for search engine. Compare indexed pages with others and try to find difference, look at similar sites indexed on that search engine, and try to find difference. That is the best way to find what is wrong.
Everything fixed? Site made for visitors? Resubmit to search engine, or, if site is spidered regularly, penalty could be automatically removed.
One more reason for above (only a few page indexed) could be that pages are "lost" in SE database, and not included after updates. Try to resubmit (a few days in a row, once at day) one page what is not included in listing, and see what happens.
New site (domain) penalty
There are more and more new sites every day, thanks to the spammers, more than search engine can swallow. So, Google TrustRank (and supplemental index), and Yahoo new site penalty is something what was necessary. What means, today is not easy to get good rank with a new site, you need to be a good guy at least one year, building links popularity slowly and adding new content naturally. Yes, there is a way to launch new site to the top, but I don't recommend those methods. Fast come, fast go.
Duplicate content penalty
Although I have a two similar sites (some pages are copies, others very similar) for test purpose, both sites are indexed and listed on search engines. Difference in ranking is present (domain name,link popularity..) for similar pages. Duplicated pages are not listed, only one copy of each, on more popular domain. What means, duplicate content filter is in action. What means, if some of your pages are not indexed or they are banned, look for content theft, or change that page enough (optimize) to get it little different from stolen copy.
Many articles are downloaded from article directories, and posted on web sites. That is duplicate content. But, when looking for something using Google, you can see many of those sites listed on search engine results page, with the same article. Although that is duplicate content, there is enough other content on the same page to avoid duplicate penalty.
One mistake webmasters are often doing is not to add permanent redirect from old domain to new. Copying pages to the new site and the same content left on old site. Search engines don't like twins, and one site will be filtered.
Duplicate content penalty is nothing other than duplicate content filter. For SE spider, older document on "stronger" domain is original, what is not in all cases. What means, once written, page must be left as is, or copycat will boost his rank with your copy, and your page will finish in supplemental database (what happened with a few pages from this site)
Google thinks (for now) that is not good, say, to have an exact match in title (keyword=your page title). That is only one of factors. It seems that google spider can recognize SEOed page (page optimized just for ranking, not followed by quality content). For very competitive keywords, be sure that human review is involved and filters applied according to quality of website. There are many other filters, including manually applied penalty to just one page.
Latest Google Panda updates (Penguin, WebSpam), for example, killed position of many good websites, due to a few bad pages.
Web site banned?
If your site is banned from search engine (no pages indexed) and SE spider is sniffing index page only, you need major overhaul.
If it is a new site, or if domain is moved to an other host, it will be good to check IP address of that site. In case that IP was used to spam search engines before, it can be that IP is banned. The same is with domain name, if it is not new. Try to send email using form on your site to some known Hotmail account. If it is not received (blocked), you can be sure that IP or domain is blacklisted on MSN search.
If your site is "clean", made for visitors, try to contact that search engine staff and ask what is wrong.
Or maybe not?
If only index (main) page is indexed, and there is no SE spider activity on other pages, could be problem with link structure (spider cannot follow links). Try to submit simple sitemap, or add simple text links to pages, to help spiders. Your links are maybe not SE spider friendly. This can be confirmed if there is link from other site to some page on your site. If that page is indexed, and others linked from that page are not, there is, for sure, problem with internal linking.
Or maybe you deserve that?
So, you may think that you are clever gay. 100+ cheap *.info
domains bought from Godaddy, 100 wordpress blogs generated and
filled with stolen content, or maybe 100000 generated pages,
everything to get what is possible more cash, using AdSense ads.
Even then, when pages are different from other similar generated
sites, there is one big "footprint" left.
How to avoid to be penalized
No, this above is not free advice to SE spammers, this is warning to you and other webmasters, that, if you are using similar methods like SE spammers are using, your site could be banned. Many sites are banned or penalized, only because they are looking like TE (TrafficEqualizer) generated pages (scraped search engine results).
So, according to above "trend" you can expect that: *.info domains could be penalized (cheap domains used for spam), blogs could be penalized (sblogs - spam blogs), even when links are below content (in page source), that could be penalized (footprint of one spam generator software). What means, take a look at structure of default generated page from SE spamming tool. Avoid that page structure if it is possible, because, many SE spammers are too lazy to change that structure, and that is big "footprint". That "footprint" could affect your sites, especially if there is no quality links from other sites.
There is something what we can call critical mass. When one kind of websites (read spam) are starting to dominate search engine results, it is naturally that algo will be tweaked to filter that kind of spam. When one method of promotion becomes popular, it will not last long.
Every search engine spamming method what show results, and can be obtained for free, is unuseful later. Don't play with that.
What about articles, now very popular kind of promotion? "Keyworded" articles are one kind of spam, and they will be filtered first. Almost every SEO method what is overused will be, and it is filtered on some way. Link spamming is the current.
Want a proof? Doorway pages, then "directory sites", MFA, now sblogs and link spam, just a few most popular. Average life of any search engine spamming technique is one year. You have enough time to think about.
Your worst enemy is the...
...sneaky competitor. That kind of people you already know, they are your friends today, and your enemies tomorrow. That kind of people you can recognize if you are reading SEO forums. Questions like "can I submit SPAM complaint, this website is using this (not spamming method)" . He maybe found one hidden link, or fonts in same color as background, but he doesn't care about real spam websites below his website position. Because he don't know how to optimize website better, he is trying to pull other webites down using everything he could. One more reason to keep your site "clean"
If you think that above is something bad, prepare for worse. If search engine position of your site is "floating" from top to bottom and back, that could be from two reasons. First, search engine is testing new algo, or it is updating index, so positions of listed sites are "dancing" . Second reason is that your website positions is attacked from competitor who is using search engine algo (algorithm) bugs. There is no doubt that your site will be treated like spam site (although "clean") if competitor decides to use those bugs against you. This includes backlinks spamming mentioned below.
Check your website logs, especially if you are using some kind of open source CMS. Check for keywords not connected with site theme, check for suspicious 404 requests (generic attacks), check links FROM your domain (maybe you have a page full of links to spam sites, and you didn't put it there?) keep an eye on your blogs comments and scripts, and read underground SEO forums.
You know how many websites are linking to your website, don't you? Although Google said that links from low quality websites (links farms for example) will not hurt, they simply will be ignored, since you cannot control who is linking to you, don't believe in that. If your website receives 10 000 links from blogs, forum profiles and other suspected sources overnight, that will hurt your backlinks profile. In case of high authority website, with many quality backlinks, impact will be low, but for small site with a few quality links, that could hurt.
So, advice? Good old static HTML page is still working...
Avoid any method of search engine optimization or promotion what could raise red flag. Once your website if flagged, or banned, it is very hard to back it to the SERP. Submit reinclusion request only if you are sure that everything is right with your website.