Welcome to the Q&A Forum

Try putting your url into this site, it can help detect whether you have been hacked:

http://sucuri.net/

That should help determine whether you've been hacked, and what might be causing the problem.

The issue could also be that there is some plugin that you have installed that is causing the problem. Try disabling all your plugins and see if that fixes your problem. Then re-enable them one-by-one to determine which one is the culprit.

I think Penguin is the penalty you're thinking of (Penguin targets links, Panda targets low quality content).

First of all, if you are manually building backlinks, avoid getting too many exact match anchor text links. So, if you're trying to get a page to rank about "cheap real estate", avoid having too many links that have that exact anchor text, because it looks unnatural and you could get penalized. The latest Penguin update penalized sites with as low as 50% of links with exact anchor text.

The best way to avoid link penalties is to get links where you can't control anchor text. These include things like organic mentions on newsites, blogs, and magazines. Instead of thinking "how can I build more links?" think: "how can I create content that people will want to link to?" Those are the links that are going to carry the most weight anyway, not random backlinks from unrelated sites.

In my experience, Google still treats subdomains as separate sites in many respects (I work for a large ecommerce site with 30 different subdomains). It's also how large webhosts like wordpress.com & tumblr.com can get away with having so many people creating poor content without being penalized-- each subdomain is treated as a separate site.

If you want your site to get SEO benefit from your blog (and vice versa), I would stick to subdirectories. Why take the chance on a subdomain? They certainly don't provide any benefits above and beyond a subdirectory.

There are a number of different keyword trackers out there, which one you want to use will depend on how many keywords you want to track.

For a small number of keywords, SERP Fox is a great tool for $10/mo: http://www.serpfox.com/

Another good tool is SEO PowerSuite: http://www.seopowersuite.com/

If you're tracking thousands of keywords, you might want to check out Authority Labs (http://authoritylabs.com/) or LinkDex (http://www.linkdex.com/).

User behavior on your site is definitely a ranking factor, although no one can say exactly how large it is. It is theoretically possible to manipulate this, but it is perhaps not as easy as you make it seem.

You would need multiple people clicking in from different computers and different IPs. Also, Google doesn't just look at CTR, but time on site and how the user interacts with your site, so your contractors would need to act like actual visitors to your site. Then this would need to be done with enough volume to actually make a difference. Maybe that's not so difficult with a low search volume term, but good luck trying to make a meaningful difference on a high volume term. And again, no one knows how big of an impact user behavior has, or exactly what user behavior metrics are counted.

So it's possible in theory, but difficult in practice. You'd probably see a higher ROI spending your resources creating new content or building links, and just having an awesome site that results in positive user behavior.

1. Yes, it's a good user experience to link back to the homepage from every page of your site, unless you're creating a squeeze page/landing page.

2. Why would you link to page with irrelevant anchor text? Not only will that not help with SEO, it's also a poor user experience.

If it makes sense for that page, it won't harm your site. It probably doesn't make sense to include the location for a contact form, though.

Microsites can be done in a spammy way or a white hat way. If you have the time & resources, you could consider posting unique content on each of the mircosites and build them up as legitimate sites. They could even draw in search traffic. Then link them to your main site in a non-spammy way (i.e. no exact match anchor text).

DMOZ, BOTW, and Yahoo are really the only directories worth submitting to, plus maybe a couple of niche specific directories and local directories. That's like maybe a dozen directories tops.

As long as you keep directory submissions to a minimum, it's not going to get you penalized, so there is no need to worry about "ratios" or anything like that, although you may want to vary your anchor text or stick to your brand name.

The bigger issue is that directory links don't carry that much value, so you'll want to acquire relevant, high authority links outside of directories if you actually want to rank.

Forum links don't tend to carry a lot of value, but they can still help. Post-Penguin it's probably not a good idea to stuff these signature links with keywords, but a few links from relevant, high quality forums can provide some value. Besides the SEO value, which is minimal, links from relevant forums can actually drive qualified traffic to your site and help get your brand out there.

Are you using Google Webmaster Tools? You will generally receive a warning if you are being penalized for unnatural linking:

http://www.google.com/webmasters/

Google Webmaster Tools also has a "disavow link" tool, which allows you to tell Google which of your links are poor quality links you don't want counted against you. You can also try reaching out to the sites that you received the low quality links from, or contact the people who provided you with the fiverr gigs to see if they can remove the links.

If you didn't have much of a backlink profile to begin with, it may be easier to just start with a clean slate and start a brand new site that doesn't have all those spammy links.

Google can easily identify navigational elements that appear on every page, and will ignore those for the purposes of identifying duplicate content. You don't need to be worried about your navigation being flagged as duplicate content, that's a standard feature of most websites.

That being said, you can be penalized for having lots of pages with little or no content (Panda). You'll want to make sure all the pages on your site provide some kind of actual value.

I did some research, and apparently trackbacks are really easy to fake (they just ping your blog with fake info). The comment "we arrived across a neat internet site that you could possibly like. Just take a look if you need..." sounds like there might have been a link there, that got cut out.

So basically spammers send these trackbacks that look like they're coming from legitimate sites hoping that they'll get approved so they can get their link posted on your site.

a & c just look at the site an evaluate it. For b, do a site: search on Google  to see if they are indexed and also see if they rank for their own brand name. For d, just don't overuse the same anchor text across multiple sites, keep it "natural".

PA & DA are tied closely to inbound links. It could be that the site lost incoming links, or the sites that were linking to it dropped in PA/DA, leading to the linked site also losing PA/DA.

Nofollowing internal links is almost never a good idea. You're just wasting valuable link juice.

Google actually just recently came out with a good guide for how to handle ecommerce navigation with lots of product options: http://googlewebmastercentral.blogspot.com/2014/02/faceted-navigation-best-and-5-of-worst.html

Also, if you have a lot of categories in you store, try to show navigation that is only relevant to the section of the store the user is in. For example, if the user is in the Flowers section, don't show a ton of links for Cellphones.

"I like the concept that a directory is good only if you would still want the link if it passed no link juice."

Yeah, I agree that this statement is pretty naive. You shouldn't expect to get much traffic from Yahoo or DMOZ. People use these directories for the link juice and the credibility boost, not traffic. Since both directories editorially approve their links, they still carry a bit of weight (although exactly how much is up for debate).

Any site that's been around for a while will tend to accrue spammy links from scraper websites and other sources. Whether that's a problem or not depends on your link profile. If you already have tons of good links, a little bit of spam won't hurt you. However, if you have relatively few links, then your link profile could be overwhelmed by all the spam.

If you're worried about the spammy links, just go into Google Webmaster Tools and proactively disavow all the spam.

The links in the footer that use exact keyword anchor text could be potentially problematic. Have you seen a drop in ranking for those keywords? If you haven't, I would recommend leaving it alone as it doesn't look particularly spammy. I would also advise against nofollowing links to your sites. If they're good sites and you trust them, then leave them be (again, unless you've been penalized or are receiving notices in GWT).

First of all, assess all your external links with a tool such as OSE or Majestic. Identify all the links coming from low quality/spammy sites, as well as the anchor text that is being used for the links. Greater than 30-40% exact anchor text links can get you penalized.

Then, go through the links and remove all the links you are able to. Use the disavow tool in webmaster tools on those you aren't able to remove. Then file a reconsideration request.

Note that because you are removing all these links, you will need to build new links to get your traffic back to the level it was previously at.