Matt & Pierre, thanks for your thoughts and sorry that this ended up being a rookie mistake. I have a rel canonical good to go. Thanks again for your time.

No worries at all--glad it turned out to be easily fixable.

And now I know what "nerfed" means. :)

This is why I love HackerNews. Guy asks for SEO help, frigg'n Matt Cutts answers!

FYI - Another fairly common usage of "nerfed" these days (especially in the gaming community) refers to something being toned-down. E.g. if many players are complaining about a character ability being too powerful, the developers may consider "nerfing" that character.

In Internet Marketing, we refer to being delisted as getting "sandboxed"

As you're replying to Google's Web Spam lead, I'm sure he's familiar with the terms for obliterating your splog farms. :)

I have also seen a messed up (404 erroring) robots.txt file cause a site to get deindexed out of the blue

That's a misconception. A 404 on robots.txt will not have any effect on crawling as it's treated the same as an empty robots.txt file allowing all crawling.

But it's different for 5xx HTTP errors for the robots.txt file. As Googlebot is currently configured, it will halt all crawling of the site if the site’s robots.txt file returns a 5xx status code for robots.txt. This crawling block will continue until Googlebot sees an acceptable status code for robots.txt fetches (HTTP 200 or 404).

interesting that needs to go into the webmaster guidelines I was not seeing 500's or having it reported in GWT as errors on the site that it happened to

It doesn't belong in the guidelines but it is described in the relevant section of the Help Center:

http://support.google.com/webmasters/bin/answer.py?hl=en&...

In summary: If for any reason we cannot reach the robots.txt due to an error (e.g a firewall blocking Googlebot or a 5xx error code when fetching) Googlebot stops its crawling and it's reported in Webmaster Tools as a crawl error. That Help Center article above is about the error message shown in Webmaster Tools.

Given that you said you did not see errors being reported, That suggests there was something else going on. If you need more help, our forums are a great place to ask.

Chears I am of on leave for a week ill get this put into our best practice guide for our devs and IS guys when I am back.

Funny thing was I tried resubmitting the main page in GWT an all the traffic came back almost instantly.

I have a question: Why are these considered different sites by your algos? If we were talking ".com" vs ".net", OK, I get it. But this is about "www.domain.com" vs "domain.com" and their http and https variants. I'm sure there's something I don't understand.

Would "http:www.apple.com", "https:www.apple.com", "http:apple.com" and "https:apple.com" be treated by Google as four completely different and separate sites also to be ranked in isolation of each other? Why?

"www" might be a very special case, but there are lots of times where "this.domain.com" is completely unrelated to "that.domain.com".

Many sites, for example give users their own "name.whatever.com" subdomain. In those cases treating the sites as the same doesn't make any sense.

True, but I think that is just the special case being asked about. Would it make sense to have an exception for “www”?

That's true, but the www/no-www/http/https cases are very likely to refer to exactly the same site. Besides, Google's algos, through crawling, should know that it is the same site. It seems unfair to punish the site for this.

Do we still have to do the redirects if we have this setup properly in webmaster tools? That is, under configuration --> settings --? preferred domain.

Second, in webmaster tools, should we always have the www and non-www setup so we can do the "change of address". For example, if www.mysite.com is my preferred URL, do I need to also make sure mysite.com is in webmaster tools and change the address to go to www.mysite.com?

My SOP is to make sure first that all non-canonical versions of the home page (the page with the most value, usually) are redirected, then make sure you set your preferred address in WMT, then add the rel=canonical tag to capture all the possible versions of the home page that you can't think of. As a side note I also noticed (the hard way) that Google treats capitalization in URIs the same way as these examples so www.Example.com is treated differently (at least for link value) than www.example.com. Basically if there is a single different character in the URI then it's considered a different URI.