Glad you figured it out. I honestly didn't think it would have been the canonicals. I'm a little surprised that the bots didn't just choose not to respect the suggestion as opposed to blanking your site from the index. Didn't think that was even a possibility from incorrect canonicals. Good to know for the future though in case anything like this comes up with anyone else's site.

Not exactly. Its not so much that the canonical "supersedes" an index, follow tag.... a canonical tag establishes equivalency while a NoIndex is more like a "does not equal." The Index, Follow is still there and being seen by bots as they crawl... in fact, if you had NoIndex on a page with a Canonical Tag, it may not even see the canonical at all since you told it to NoIndex the page. The Meta Robots Index tag comes first allowing the bots to crawl and index the page but then the canonical sets up equivalency to a separate page. So if your canonical tag is being respected, it doesn't wind up doing the same thing as a NoIndex (though it may seem that way) nor does it do the same thing as a 301 (though there are similarities in how equity is passed). Since a canonical establishes an equivalency, you'll find that the Canon Page will eventually take the place of the Canonicalized Page in search results because you're telling them the Canonicalized Page _is _the Canon Page & that the Canon page is the right version of both.

I took a look at all of the usual suspects as well... which amounts to pretty much everything that everyone else mentioned but I was intrigued by this issue and thought maybe another set of eyes might notice something that was off. Nothing was wrong in the page source from what I saw, no issues crawling it myself and I didn't see any penalties. Normally I'd think that if your homepage wasn't appearing for branded organic searches then a penalty was levied against you but when that is the case the homepage is still normally find-able in a Site operator search. M__aybe it is related to all the backlinks that were lost/deleted in the past month but I'm not sure why that would be the case unless removing the homepage from the index was a Penguin response to link issues... but I was under the impression that peguin was devaluing the link source not the link recipient and deleting/removing links seems to be a preferred method of handling penguin-related issues. So if there is a relationship between penguin and your homepage being deindexed then I am not sure at all why nor am I certain how to fix it as I'm not seeing anything in particular that screams "linking issue" at me. (though I only did a fairly cursory inspection of things)

So I am stumped. Whenever the issue is figure out I would love to know how/why this came to be.

If a URL was indexed and has since had a canonical added to it pointing to another page, it will eventually disappear from results. Basically the pages gets consolidated with its canon page. If the bots choose to respect the canonical tag in that instance, all signals get passed to the canon page while still allowing the page and information to be accessible by human visitors. As such, there's no reason to keep the page in the index because you're telling the bots that another page is the correct page instead. This is not the same as NoIndexing a page but will eventually remove a page from the index much in the same way that a 301 will pass equity along to another page while eventually removing the redirected page from the index in favor of the page being redirected to.

It is absolutely natural for people to link to your website with your URL. When looking at your backlink profile, you should see tons of links with the anchor text being things like your naked url or "website" or "this". In fact, it would be incredibly unnatural, and potentially a sign of paid linking schemes, if every single link to your website was a keyword rich, long tail anchor.

There is nothing "bad practices" about allowing a non-existent page to 404. People often times forget that a 404 isn't a signal that something is broken and needs fixing, its just a status code that returns "Not Found". Sometimes it makes sense for things not to be found on your site because they were never there in the first place. 404s eventually stop being crawled and indexed.

You shouldn't just bulk redirect things to your homepage though. Its always best to have a 301 point to the most relevant page based on what the original page was. If there is no most relevant page, have you considered 301-ing them to one step up in the site navigation? (i.e. a category page or hub page)

What call tracking platform are you using? Most of them will let you keep you main number (which is likely the GMB #) and continue to show that to the Bots while showing a different phone number to users based off of what groupings you've set up (i.e. one # for organic, one for PPC).

This may help: https://kb.yoast.com/kb/how-do-i-noindex-urls/#group

Are you using any specific seo focused plugins like Yoast or All-in-One SEO? They should have the option to update the Meta Robots tag to NoIndex, Follow.

If your Tag pages are creating duplicate content, you can go back and NoIndex those tag pages & they won't show up as duplicates in the index. It may take some time for Google to recrawl, recognize they are noindex'd and then remove them from the SERPs if they were ranking anywhere.

Google Webmaster Guidelines suggests you should "Use robots.txt to prevent crawling of search results pages or other auto-generated pages that don't add much value for users coming from search engines."

There is nothing "bad practices" about allowing a non-existent page to 404. People often times forget that a 404 isn't a signal that something is broken and needs fixing, its just a status code that returns "Not Found". Sometimes it makes sense for things not to be found on your site because they were never there in the first place. 404s eventually stop being crawled and indexed.

You shouldn't just bulk redirect things to your homepage though. Its always best to have a 301 point to the most relevant page based on what the original page was. If there is no most relevant page, have you considered 301-ing them to one step up in the site navigation? (i.e. a category page or hub page)

I more or less agree with EGOL. Directory Submissions are a thing of the past and are likely to get you in trouble nowadays. Getting backlinks is becoming harder and harder everyday. You need to diversify more and make sure that all those links to you look as natural as possible. It's not a bad thing to do linking yourself to get that initial push but the best possible linking strategy is a naturally occurring one. Make sure you use all relevant social avenues open to you... Facebook pages, G+, LinkedIn, Pinterest, Instagram, StumbleUpon, and so on as long as it make sense for your site to be there and you keep up with posting. Hopefully those will generate natural links back to your site as people learn who you are and grow to like your site.

In some cases, the capitalized version and lower case version of a search won't return the EXACT same results in the SERPs (sometimes a result will shuffle a bit [though not by much from what I've seen]) but Google does understand that "Example" and "example" are the same word much in the same way that it knows a singular and plural of the same word are related, i.e. "Shoes" will show up for a search of "Shoe" and vice versa.

If you also take into account the regular shuffling of the SERPs every time Google so much as blinks, there is the possibility that when the rankings data was pulled for your terms they were done so in a fashion that shows two different numbers that were both correct at the times they were pulled. Plus, in the past week (week and a half?) there was a decent bit of volatility in the SERPs that lead people to believe there was an algorithm change happening so for all you know that may have put an odd hiccup in the numbers as well.

Worse comes to worst you could always do a bit of testing to see if maybe you stumbled on a previously unknown traffic/rankings difference. Shouldn't be but with 500+ algorithm changes a year, you never know.

This is a very common issue. When you publish a new blog post with tags, and your tag pages are index-able, you are essentially posting the same content to two or more places on your site. The two easiest options are either don't use Tags or make your tag pages Noindex.

In the upper right-hand corner by "Campaigns & Tools" there's the symbol that looks like a Head with a few lines next to it. Click that and in the dropdown is "Billing & Subscription". On that page you'll find a link to Cancel.

Spammy domains have been known to overuse the Hyphen... but using Hyphens does not make you spammy

Matt Cutts had previously stated that Google recognizes the Hyphen as a separator and the Underscore as a connector... i.e. "red-wigdets" gets read as "red widgets" while "red_widgets" gets read as "redwidgets". For keyword purposes, a hyphen is technically better but the difference is likely negligible. Also keep in mind the EMD update. If your core term is "cheap red widgets" and your domain URL features "cheap-red-widgets" then the EMD has made the previous positive name correlation into a less powerful signal.

Matt Cutts 2011 Underscore vs Dashes in URLs video http://youtu.be/AQcSFsQyct8

Matt Cutts 2009 Underscores or Hyphens in URLs video http://youtu.be/Q3SFVfDIS5k

Matt Cutts 2005 Dashes vs. Underscores blog post http://www.mattcutts.com/blog/dashes-vs-underscores/

Social Bookmarking does still work but not as well as it may have in the past. It can still be a viable way to get traffic to your site but not necessarily always the most qualified traffic. Personally I'd say to stay away from any social bookmarking tools that will automate things for you because that will be a bit of a red flag if you're too spammy with adding your links. A more natural approach to getting your pages added to social bookmarking sites is the better way to go. Just don't expect it to magically increase you rankings, conversions, etc.

As per the Google Places reviews guidelines (link

Conflict of interest: Reviews are only valuable when they are honest and unbiased. For instance, as a business owner or employee you should not review your own business or current place of work. Don’t offer money or product to others to write reviews for your business or write negative reviews about a competitor. We also discourage specialized review stations or kiosks set up at your place of business for the sole purpose of soliciting reviews. As a reviewer, you should not accept money or product from a business to write a review about them. Additionally, don’t feel compelled to review a certain way just because an employee of that business asked you to do so. Finally, don’t post reviews on behalf of others or misrepresent your identity or affiliation with the place you are reviewing.

So I'd suggest not offering free visits in exchange for trying to get reviews (positive or negative).

In most cases Google is smart enough to understand that a page relevant for "Wood Desk" could or should show up in searches for "Wood Desks" and vice versa. As such, it's not really necessary to make sure that you shoehorn in all of the plurals and singulars of your core terms. Worry about it more from a Human standpoint. Making the title more human accessible will help with clickthroughs, visits, and so on. Forcing multiple variations of the same word into a title in order to attempt catching every variable will probably make people skip over you. And ultimately, getting the qualified traffic is what much of SEO is about.