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I totally agree with Federico about creating great content. That would be exactly what I would have suggested as well.

There is the possibility that something got messed up on the back end too if you believe you are already making great content. Are you positive that the markup is still on the site?

I think I understood what you were asking and I thought you could extract some information from that video.

Let me try to clarify though.

Normally, site wide links are bad, even if its only one site to another and not the other way around. You could argue that they add value, which is why I linked to the above video, since it seems like that is a hard case to make (I don't know the site, I am just assuming).

So, this is really a bigger issue of value add. If it does add value, you could make a case that they should still be there.

That said, even in that situation where it does add value, the link should still probably be a no-follow since Google will likely interpret this as a spam signal or just simply trying to "beat" them at their game.

We had an interesting situation here at the office where a client had a legitimate page on the site mysteriously vanish. Still investigating.

I am guessing its just a glitch. If it still hasn't resolved itself, contact the moz team (http://moz.com/help/contact) they are super responsive and helpful when you need something.

I just checked it myself, and It is in fact showing up for me...

So if you are concerned that the homepage isn't indexed, it is.

I don't think you "need" to add anything there. There are no hard and fast rules. But having some sort of navigation there is a good idea.

Think about adding:

Home, About, Company info, contact, etc... those are the basics.

Also, if you want, consider adding in the main top level categories that are important. I think Zappos does a good job of this.

It really depends on what your strategy is here, but I would strongly look into revamping the kind of content that you are publishing and focus on something that your audience is really looking for.

While the social shares are nice, the links are important. And I am not saying there is no value in the social shares, but with those kind of numbers, I think there is more you can do to possibly improve on the content, and make it slighly more targeted to what people are looking for.

I would even go as far as to say, that the links are not the only reason you should be writing. It should be more around thought leadership, attracting a bigger more committed and passionate audience.

Content for the sake of content is not a good practice. It makes it thin, and then you have bigger problems

One of the major value adds with Wistia is the analytics and customization. I think they look really nice and you have a lot more control over the details.

Youtube, is obviously about the reach, simple sharing, etc.

It makes a difference what the goal of the video is.

And depending on that, I am not necessarily sure I would worry about the snippit showing up. Google has seemed more biased towards that lately.