I've seen this happen where a site buys an EMD and then names their company after it and then subsequently gets links that are branded but in reality they are only branded because they were lucky enough to buy an EMD.  Does that make sense?  For example, if someone wanted to start a house painting company in Anycity and they see that anycityhousepainters.com is available then they name their company "Anycity House Painters".  The branded links that come to them are indeed branded...but they're also an attempt to manipulate the serps.

I think that if you have a brand name that is the same as a keyword Google may not look at it as a brand name.

As far as "balancing this out" goes, it depends on whether or not you've really been penalized.  If there is an unnatural links penalty then that needs to be dealt with.  If there's a drop on a Penguin refresh day, that's a whole 'nother issue.

It's also possible that the drop has nothing to do with the branded links.

But, I think that Scott gave you some good advice on ways to link to your brand.

I have a story as well about something that happened to me today and it is relevant to your question.  We have a real estate site and today we started getting hits for "top realtor in [city]".  I was trying to figure out why because we haven't optimized for this at all.

Well, it turns out that I recently wrote a silly blog post called "Top 5 videos about....", and I also had a post on our site called "Top 10 neighborhoods in [city]".  The fact that the keyword "top" and the keyword "realtors" and the keyword "[city]" were on our site actually makes us rank on the first page for "top realtors in [city]".

The more content you have on your site the better!  As a result of this discovery today I actually rewrote our home page to include more keyword phrases that I want to rank for.  (You have to be careful to write for readers and not just search engines though.)

Google's Above the Fold Page Layout algorithm looks at how much good, helpful content is visible without scrolling:

https://webmasters.googleblog.com/2012/01/page-layout-algorithm-improvement.html

There is often a struggle between designers and SEOs because it sure looks nice to have a big huge image taking up all of the above the fold content but if there is no or limited helpful text there then that's not good from an SEO standpoint.

With that said, Google will still index content that is below the fold. It's debatable whether it's given the same weight as content higher up on a page though. Matt Cutts from Google has said before that a link that is higher up on a page is not worth any more than a link lower down on the page. However, some experiments by Moz contradict this.

This might be a fun experiment to do - create content both above and below a hero image and see what ranks best. I might even do that!

Marie

While it could be Penguin, I don't think we can make that call on the data given to us in the question.

I definitely agree that Penguin is a huge possibility.  But, I think it could be dangerous advice to send a site owner on a link removal/disavow mission when we don't know for sure.  There are many other possibilities.  It could be a Panda issue.  It could be that it was a new site and the previous high rankings were a honeymoon effect.  It could be that the /home.html page is blocked by robots.txt or has a canonical tag that is confusing Google.  It could be that they changed the title tag on the page so that it is no longer appropriate.  It could be that the site was hit with malware and users are clicking away because of virus warnings.

(btw...the thumb down was not from me.  I respect that you are trying to help but just wanted to comment to make sure that the site owner (or someone else reading this post) doesn't go off disavowing links without getting to the cause of the problem first.)

I would disavow the blogspot subdomains individually.  So you'd have 1000 lines that say:

domain:subdomain-name.blogspot.com

The documentation for the disavow tool (http://googlewebmastercentral.blogspot.ca/2012/10/a-new-tool-to-disavow-links.html) says the following:

Q: Can I disavow something.example.com to ignore only links from that subdomain?
A: For the most part, yes. For most well-known freehosts (e.g. wordpress.com, blogspot.com, tumblr.com, and many others), disavowing "domain:something.example.com" will disavow links only from that subdomain. If a freehost is very new or rare, we may interpret this as a request to disavow all links from the entire domain. But if you list a subdomain, most of the time we will be able to ignore links only from that subdomain.

What we don't know, however, is if we can do a disavow:blogspot.com to get everything from blogspot.  I wouldn't trust it to do this and I would definitely disavow each individual subdomain.

If you don't have a manual penalty then there is no way to upload anything other than your disavow file to Google.  Your disavow file is not read by a human.  It is machine processed.  You simply need to trust that you have done a thorough job and then, when Penguin refreshes, if you've got a good base of good links you should see an improvement.

You may want to watch this Google hangout: http://www.youtube.com/watch?v=7NNf_AhA1gw&feature=share&t=42m25s (42:25).  The question is exactly what you are asking.  John Mueller says that if you are showing Googlebot your full content but users can only see it by logging in then that is cloaking and is against the Google guidelines.  If you show a snippet of your page to users and Google sees the same snippet then that's ok.  He said another possibility is to use "first link free" where you allow the user to see a limited amount of content and then put the rest behind a paywall or other type of a read gate.

I'm also in agreement with Egol in the fact that putting content behind a read gate could really turn away users.  I hate it when I search for something and find what looks to be the perfect answer to my question only to find that it's behind a gate.  The result of this is that I immediately click away.  And, for sites that I know regularly have gated content, I won't click on them at all in the search results.  If this type of user behavior happens often then there's a good chance that it will be seen as a sign of low quality and the Panda algorithm will affect your site which could result in drastic drops in rankings across the board.

The answer to this depends on what kind of a link profile you have.

I have some clients for whom I do monthly disavows. These are sites that had a long history of unnatural link building and even though they're not currently building links, there are a lot of old links that keep surfacing.

For others I do a quarterly link audit and disavow. These are great for two reasons. One is that we keep the link profile clean but the other reason is that we get to see what new links are pointing to the site. I am often able to catch problem areas. For example, perhaps a new team member has started to venture on a link building tactic that's a little on the grey side. But in other cases, I can point out the really good links that they are getting and advise on doing more outreach to that content or perhaps building similar content.

If you are a regular site that has not been overly involved in low quality link building in the past and are not in a competitive space where you're really worried about negative SEO, then reviewing your links every 6-12 months is probably good.

I definitely vote for one big site as well.  I think every person has this idea that multiple sites will help because you will be able to crosslink them.  But the juice you get from those cross links is less than the juice you would get from having all of your links pointing to one site.

I would have one main site and then have 3 folders within the site each with their own focus.

There are a few ways.  If you have the SEOMoz toolbar installed, you can click the nofollow button and it will highlight all of the nonfollowed links in pink for you.

Or, you can check the source code.  To do this right click on the page, and select "view source".  then, do Ctrl-F and search for "nofollow".  This will show you if the whole page is set to be nofollowed (i.e. meta robots noindex, nofollow) and if an individual link is nofollowed.

As a side note, I don't do much article submission.  I do believe that the links from ezine are followed, but the link juice you get from them is usually minimal.  The way that an article would have more link juice on ezine is if other people from high PR sites linked to it.  But, if it's that good an article that it deserves links then it would be much better to have it on your site.

Similarly, forum sigs are usually not terribly helpful for ranking unless you are targetting a really,really non competitive term.

It's funny you should mention this today.  In the past I've always been against boosting your facebook or twitter fans.  I'm seeing some benefit now though.

As an avid user of facebook, if I see a page that has cool stuff and is followed by thousands of people, I am more likely to follow it.  I'm  not as likely to become a fan of a page with 100 members even if the content looks decent.

I'm experimenting with spending a few bucks on facebook ads to increase my fan base.  These would be truly targeted fans who want to connect with me and my product.

I am finding that I am building some good relationships via facebook and getting some conversions as a result of my fan base.

Plus it's kind of an ego boost to post something and see a bunch of people liking and commenting on it.