Some of the reasons why a site goes into the supplemental index of google are:
What exactly is the Google supplemental index?
Google indexes around 3.3 billion web pages and that’s a something huge. The search engine giant has set some parameters on the basis of which pages are crawled and indexed. Now Google has 2 web indexes, one is the main index and the other is the supplemental index. When for some reason Google feels that a particular page cannot be included in the main index, it puts it in the Supplementary Pages.
So are the pages in the supplemental index penalized by Google?
A big NO! Supplemental index is not an index of penalized pages, nor is a trash bin. As the search engine has to index billions of pages, they have set some quality parameters on the basis of which they include pages in the main or in the supplemental index. Many new pages go supplemental just for the reason that they don’t qualify enough to be in the main index.
What are the reasons for supplementary pages?
There are quite a few reasons for pages going supplemental. Those are:
Duplicate Content: This is one of the main reasons for supplemental pages. If pages share the same content, then one of those pages will surely make it to the supplemental index. The page which will be in the main index depends on some factors like page rank, backward links etc.
Same page Title and Description: If there are pages that have the same title and description, then many of those pages have a high chance of going supplemental. So it is always advised to keep page titles and description unique.
Canonical Issues: If there are 2 versions of the same page, one with WWW and another without WWW then one of those pages will go supplemental. It’s better to solve any such canonical issues with a 301 redirect to avoid pages going supplemental.
Lack of content: Give the spiders something to chew on. If a page has only images and lacks content, then most likely it will go supplemental. So you need to have a good combination of text and images on your pages to avoid the supplemental index.
Lack of Page Rank: This is also one of the factors that lead a page to the supplemental index.
Orphan Pages: If there are pages that are lying orphan, which means that the pages are not linked with the rest of your site, then the pages will so supplemental. So you should have a clear navigation in your site and make sure than none of your pages lie abandoned.
Dynamic URLs: If there are too many parameters in an URL then the page has a high chance of going supplemental. Dynamic pages are never preferred by the search engines, even though Google can index those pages. It’s best to rewrite those dynamic URLs into static ones. They are far more search engine friendly than dynamic ones.
Even after all these, pages can still go supplemental for some reasons that are known only to Google. But these reasons are the most common ones for supplemental pages.
You don’t need to be afraid of your supplemental pages. Use solid white-hat techniques for optimizing your site and build your site for your visitors, not for the search engines. Voluntarily link out to some related authority sites on your topic, this will help to increase your site’s trust rank and overall quality score. Sites having higher Trust Rank and quality score seem to avoid the supplemental index much easily.
At the end, I’d like to mention that even the personal site of Matt Cutts, head of Google web-spam team has some of its pages in the supplemental index and so are pages of Yahoo and MSN. So there’s not much to worry, Google will pull out your pages of the supplemental index once it finds those pages worthy enough to be in the main index. So have great content and build links from quality and related sites.
Follow the above points and surely its going to help your site come out of the supplemental index of google.
Getting Out of Google's Supplemental Index-
Supplemental indexing is, to a degree, a matter of trust. So the first question you have to ask yourself is, Am I absolutely positive there are no other "trust" reasons why Google would toss my pages into the supplemental index? Have I done anything suspicious in the past? Has my webmaster or SEO expert done something wrong?
Assuming the answer is NO, here are some ways to help get your pages out of the supplemental index:
1. Eliminate the duplicate content issues on your pages. Page TITLE and meta Description tags should be unique (and meta Keywords, too, if you use it). Try to limit as much duplicate content as possible. It's okay to have a common header, footer, and site menu on your pages — as long as your pages have enough other content to offset the common stuff. It's not okay for your red widget and blue widget product pages to have the same exact product description and page content, with the exception of the color.
2. Improve the content on the supplemental pages. As mentioned in #1, pages with little or no content are strong candidates to land in the supplemental index. That's especially true if the amount of duplicate content (header, footer, etc.) is substantially more than the non-duplicate content.
3. Improve your site architecture. If you have pages that are 4-5 levels deep (i.e., below or away from the home page), redo that structure so the pages aren't buried like that. Make it easier for the crawler to reach all your pages.
4. Improve your internal linking. Have a site map that includes links to all your pages. This'll help make sure pages don't get orphaned. Be sure to link to the site map from your home page so the crawlers can find it — and all those links — easily.
5. Fix your link profile. Who you link to and who links to you impacts the level of trust Google gives you, and less trust often equals more supplemental pages.
6. Fix your URLs. Do you really need to pass 3-4 variables in the URL? Cut down on the parameters. Keep your URLs as simple as possible.
7. Are you a theft victim? If someone has stolen your content, it's possible Google is ranking the stolen content on the other site instead of yours. Use a service like Copyscape to check for content theft. Plagiarism Today is another good resource to learn about stopping content theft, with specific instructions for contacting the offending party/parties.
8. If all else fails, take drastic measures. Rename/save all the supplemental pages with a new URL and link to the "new" pages somewhat prominently on your site — the site map idea mentioned above would be a good start. And then do a 301 redirect from the old URLs to the new ones. (This is obviously a lot of work if you have a lot of pages in the supplemental index.)
9. And finally, tell Google what's going on. When you're convinced you've exhausted all of these issues, use Google's Webmaster Central to submit your URLs directly into Google's brain.
And no matter what path you take to fix the problem, be patient. Google isn't known for quick reflexes when webmasters push to get pages back into the main index.