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It's sounds like you have a pretty good idea of what happened. The reason that Google is not emailing you in the GWMT interface to keep from giving away too much of their recipe.

It sounds like you are already thinking about the links you contracted. I would review the work you have done (or had done) on this site and review if it was the best practice and how easy the footprint would be for Google or another search engine to hone in on.

If you are not completely sure what was done or what got indexed you might want to review a tool like:

http://ahrefs.com/ or the link analysis on top pages vs yours with the SEOMOZ link tool.

Good Luck

I think it is a little early to do a universal 301 redirect of all of those sites to your main site. Some of my sites affected last month have already started to come back. I would try to continue to get them to come back a bit.

You could get some more topical content on them and maybe clean them up a bit.

Then wait.

If that still does not work and you don't want to maintain or track them you could do 301 redirects. I dont think you will pass any penalties. I have done this myself and did not see any ill effect.

It seems that when penalties happen they tend to be to a directory or a domain. The penalty does not seem to get passed along.

Anyone else seen any bad things happen when a 301 redirect was done?

What I like to do is occasionally research, work on, and perfect a solution to a problem.

Then I will have plenty of material for both internal and external content. You can first write a blog post or article on your site. And edit it a bit and have it looking good.

Then show it as the example to other webmasters and podcast hosts.

They get an idea of how you feel, know if they want your content on the matter on their site and then there is a natural page to link to for any story they do on you.

It seems like a good way to go and this then has otehr strong pages with links to you that are ontopic, relevant, and different content than the first article.

The second, third, or fourth article get easier and easier to write. And doing a podcast is a walk in the park after all the research and reporting.

I might be a little different than some of these answers but I would recommend that you exclude them from getting indexed.

The reasons I would do that are that:

You know it is largely duplicate content and goes down to the same pages as your categories.

Google has stated that they would prefer to not have it indexed.

The increasing number of pages indexed will dilute the link juice of the entire site.

There is also the possibility that people using the url bar of their browser will start to increase the number of pages indexed by a large manner.

A competitor could create thousands of links to these pages and create a huge footprint that is search pages.

And finally, I like having product pages ranking highly if at all possible.

I would do this with both the robots.txt file and the GWMT exclusion on /product/search/ directory

Good Luck!

What type of platform is this? If it is Wordpress there are solutions that do things similar to this. But Keyword Density is not as important as it used to be.

If it is Wordpress please say so and I will add the plugin names.

For the Crosslinking I use SEO Smart Links which you would have to add trigger keywords and then the page to go to as you want them added.

But then they are setup and work on all pages.

http://wordpress.org/extend/plugins/seo-automatic-links/

For the SEO Inclusion and help finetuning I have used

BloggerHigh - pretty good

But there is also

SEOPressor

Easy WP SEO

and WP SEO Automation

But those programs are not required really. I would check the template, set the permalinks, and start All in One SEO Pack. That would be most of the way there.

It seems to me that your test is a little different than how most people would consider SEO.

Most considering higher rankings and more traffic as a success. You are considering a higher percentage of pages as indexed as a success.

I think you should step back and rethink this test. With millions of pages the indexing of your site might get better and your rankings get worse with the same changes. That would probably turn out to be a net loss in benefits and actionable traffic.

I would use SEO and page content for higher rankings.

I would think of linking patterns (internally and externally), site structure, website coding and less redundant content as the way to increase percentage of pages indexed.

I agree with Syed said and might add that I have not seen Brightcove videos in universal search in Google. Has anyone else? I would go with what you are seeing. Youtube, metacafe, and vimeo seem to show up pretty well. Youtube seems pretty strong and if you upload HD the quality is pretty good.

I would also drop back into Google Webmaster Tools and see if your video sitemap has any errors. Might do that now but I also think you should consider a more mainstream video hosting service.

I might be a little different than some of these answers but I would recommend that you exclude them from getting indexed.

The reasons I would do that are that:

You know it is largely duplicate content and goes down to the same pages as your categories.

Google has stated that they would prefer to not have it indexed.

The increasing number of pages indexed will dilute the link juice of the entire site.

There is also the possibility that people using the url bar of their browser will start to increase the number of pages indexed by a large manner.

A competitor could create thousands of links to these pages and create a huge footprint that is search pages.

And finally, I like having product pages ranking highly if at all possible.

I would do this with both the robots.txt file and the GWMT exclusion on /product/search/ directory

Good Luck!

I think it is a little early to do a universal 301 redirect of all of those sites to your main site. Some of my sites affected last month have already started to come back. I would try to continue to get them to come back a bit.

You could get some more topical content on them and maybe clean them up a bit.

Then wait.

If that still does not work and you don't want to maintain or track them you could do 301 redirects. I dont think you will pass any penalties. I have done this myself and did not see any ill effect.

It seems that when penalties happen they tend to be to a directory or a domain. The penalty does not seem to get passed along.

Anyone else seen any bad things happen when a 301 redirect was done?