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Well, for one, someone mentioned guest-posting. But then, guest-posting where? What if the blog is iffy? Would PA/DA give a solid indication of this kind of thing? Or, for example, I know to stay away from "buy 40 bajillion backlinks for $3" and such, but what about an offer for an individual backlink from a high PR page, manually added potentially in the context of a guest post? Part of me thinks "okay, seems reasonable", but part of me thinks "if this is being offered then could the fact that it's being offered to others then pose an issue based on the appearance of high volume"? Also: if there is the potential for "negative" SEO, wouldn't this be easily abusable? What's to stop me from blasting 60000 backlinks to one of my competitors?

It's tricky, honestly - even if the content is legitimately/legally syndicated and provides user value, it's still possible for Google to consider it "thin", low-value content. There are a lot of caveats, though: (1) It's possible for two or more sites to both rank for a piece of content, but the winner usually depends on a mix of signals, ranging from Google's best guess as to the source to the authority of the domain. In some cases, it's possible for a strong syndicator to outrank the source. (2) It really depends a lot on your content balance. If you use partially-syndicated content in pages with some unique content, you're usually a lot safer. If you use a small percentage of syndicated content across your site, you're also usually pretty safe - worst case, that content may just not rank or get filtered out. The problem is when you rely heavily on syndicated content - it can make your entire site look low-value and trigger issues with Panda. (3) It depends a lot on the type of content. Many resellers use OEM product descriptions, for example. These pages often don't rank well (as they're plastered across the internet), but it's unusual to see them harm the entire site. If you have a blog that's just re-posts from other blogs (even completely legit ones), though, Google is just going to see your site as a copy and low-value. If the content is solely for users and doesn't have SEO value for you, you can always NOINDEX it or rel-canonical to the source (cross-domain). That will prevent an risk. Usually, though, it does have some SEO value, so you don't want to block it entirely. In that case, I would just say proceed with caution. Content syndication is perfectly valid, but you don't want to over-use it.

Thanks for updating on your findings. That is interesting, but glad you got it sorted.

You are indeed an optimist. Thanks

You are very welcome!

So, you want to create satellite websites and then get link back from those sites to your main website right? Sorry to say, but this looks like an attempt to game the SERP by artificially boosting ranking of your websites. Moreover, it is highly likely that you are going to slap those satellite sites with thin content that nobody likes, believe me search engines have started hating them too. Ok, let’s imagine that your main ecommerce website somehow manages to get some value from these inbound links coming satellite websites. But what if a Panda refresh gets the network down and the link juice that your main website has been getting so far will be smashed in a matter of second. All your hard work will go in vain. And please do not ignore Penguin. Your main website could come under the scanner of Google for building links unnaturally. So, here is my suggestion. Rather than wasting your valuable time and money on building something worthless why not make your existing website AWESOME. You can build a great blog and starts sharing great content that will help you earn Links naturally. There are other things to do. Invest in making your website more conversion oriented, reach out to great bloggers and share your expertise in the form of a great article or tool or whatsoever. In short, start adding value to your website rather than chasing the crappy links and you will be good.

Yes it did become more complex and will continue to do so. However SEOmoz has always for the most part suggested building for the users within Googles guidelines. I like to think of Google as the God of information and its rules as a bible that SEOs need to follow... Just like the bible everyone interpits it in their own way and tries to be good...

The common thought is search engines consider the sub domain as an entirely different website, but your sub domain may be your competition.  If you are selling yellow widgets on example.com and you are selling widgets on affiliate.widgets.com, you are competing against yourself. Many of the errors and warning you are getting may be affecting just the affiliate.example.com. If you site at affiliate.mysite.com, search engines probably recognize the content in the iframe as belonging to the Affiliate Company's website. I believe you can do the diagnostics here for separate sub domains.  That may help your focus on your controllable content.

That was the original email - Google has detected evidence of unnatural link building. We're still not entirely sure what caused the issue. I assume it was in our last reconsideration request but at that point we were just hoping.

Search branded and non-branded terms for the site on Google to see how the site performs. If they aren't deindexed or performing poorly for their targeted keywords it probably wouldn't hurt to obtain a link from them. However, it would probably be better to put your guest post efforts elsewhere.

Well that's good news...and a little bit strange too!  It's possible that there is a Penguin update in the works, but there's no official word as of yet. I'm tempted to think that there was something other than Penguin going on here.  But, regardless, I'm glad to hear you are ranking again!

A great way to build links to your site is to first seek to understand what content your audience wants (especially influencers and linkerati) and develop that content. Then look for ways to promote your content to people who have sites and tend to link to awesome content. People are more likely to link to content that is tremendously valuable or relevant. Developing relationships with key influencers in your niche can help a lot. Look for ways in which you can help these influencers before you ask for a link. Remember it is a marathon, not a sprint!

Maybe another factor is how if other people complementarily link to your site without you knowing they aren't necessarily thinking about your SEO, so an exact match provides automatic anchor text?

If coming from a 404 page, the link does not matter. I am not sure that means that Google did it, so I would show the 404 in any evidence you send to Google re resolving the issues. For getting reconsideration, you need to show you did all in your power to remove the BS links, etc. Keep a log. Send it all. Good luck,

When I try that tool it completely malfunctions for me....doesn't do anything. I think it's a moot point though. If you previously had pagerank and now you've gone down to either 0 or N/A then there's a good chance you've got some kind of penalty. Do you have any indication of whether traffic has dropped?  If you don't have analytics you can possibly get information from your hosting company and server logs.  Pagerank (PR) really doesn't mean much...but a loss of Pagerank plus a loss of traffic makes some type of penalty a big possibility. The question is whether it is a manual penalty or an algorithmic one like Penguin or Panda. I really would advise setting up webmaster tools today.  You can either wait and see if a warning pops up or if you feel that traffic has dropped you could actually file a reconsideration request.  Google will respond back within 3-14 days and let you know whether you actually do have a penalty.  If so, then the nature of the message should help us know what the problem is.  If not, then we go looking at traffic data to determine whether this is Penguin or Panda. OR..............it's possible there is something else such as a robots.txt problem or something else going on.  But really, without some type of traffic information and without knowing if there is a warning in webmaster tools it's going to be hard to diagnose the problem.

Thanks Donnie and Oleg - good advice there! Couldn't believe how many dodgy sites were hitting this particular site. Around 15% of links (out of not many links - around 300) from dodgy outfits all doing more or less the same kind of stuff.

This could also be that they have some app that Google shows for them through the reseller program: https://www.google.com/enterprise/marketplace/categoryHome?categoryId=2 I am not aware of a preferred SEO or SEM agency. The only instance I know of around Google and Preferred is the preferred API pricing of Adwords Certified Agencies. Best. I think your discretion as to the name is well thought out: I would send a screen shot to Google if it were me.