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Way Way Way back Google penalized a well know company that I believe were selling gifts and also owned 5+ others sites that basically took the first half of page 1 for major keywords.

Google's terms and conditions suggest not doing this, especially if you are already targeting the same niche or similar with similar content. If asked by Google would you be able to explain it that would not sound like you were trying to game the results?

HOWEVER! So many sites are getting penalized so easily these days that you would have to be a fool not to have backups. This is the very bad side to slow and sometimes impossible recoveries that many site owners have been reduced to owning multiple sites because anything can happen.

YES it will still navigate to the link,

All you are telling Googlebot is that you do not endorse/trust the link and should not pass Pagerank/link juice to it.

If the page has a noindex meta tag then it will not index it, however it will still keep coming back to that page to check if the status has changed in any way. Same with a nofollow meta tag.

Google pretty much visits every page it can.

For countries where it is not possible, I would suggest if you must have the domain, a cheap virtual office is an option to take. This way you have an address in that country to use. Not many people know about this option.

I agree Penguin 2.1 update came out on the 5th.

You need to log in to webmaster tools http://www.google.com/webmasters/tools/ check to see if there are any messages for your site to determine the severity of the problem. Also check under the left navigation "Search Traffic" -> "Manual Actions"

Let us know what you find

Send me the link I will take a quick look

Do those domains interlink and provide juice to the main site?

I mostly use companies in the UK and Canada so I would suggest you look here for a great list of trusted companies

http://moz.com/community/recommended

Find a good PR company and let them do the hard work. They have the contacts and the experience, letting you get on with creating a great service and website.

I remember speaking to a great one but will have to dig through some email but they are on that link above.

Lets say your site is using php?

Your system no doubt picks up the parameter with a php get and stores it as a session variable.

That is likely all that would need to be done before the page is 301 redirected.

Best thing to do is create a test page with the cod mentioned above on your site and try it

xyz.com/test.php?affif=12345

have the page redirect to the homepage and see if that affiliate code is stored.

If i am not mistaken, this is what you are looking for?

https://developers.google.com/webmasters/ajax-crawling/

Absolutely, many sites go through a total re-branding.

The history of the site and probably the existing back links will get the site going rather fast, providing the site has not been penalised or anything like that in the past or suspect link building.

Make sure you create a good sitemap and have a good 404 page setup for all pages that no longer exist. be sure to remove all the pages that you no longer want/need.

Take advantage of some of the existing pages on the site if possible, the history and any links to those pages will be a good start for those pages.

Also look at the possibility of 301 redirecting any pages that have pagerank or links coming to them to related new pages that you create.

I am seeing this a lot recently.

Do they have any good social mentions/activity?

DO NOT interlink your sites with dofollow links, Google hates this kind of activity and can penalize both sites for this.

It is a blatant attempt to self promote your own site and will be seen as a paid link. If you have a good site, I would not mess with it.

I would look at better ways to integrate the eCommerce site into the current existing site, why do you need a new site with a new url?

Those are know as "Sitelinks"

Here is the official page from Google about them, https://support.google.com/webmasters/answer/47334?hl=en

"At the moment, sitelinks are automated. We're always working to improve our sitelinks algorithms, and we may incorporate webmaster input in the future." Google

Having a good linking structure that is clear on your site, will help promote that. However you will also only get sitelinks when your site is an authoritative source for that search term.

I have done this many times before and had some great success.

However.... Panda targets low quality thin content. If you are going to go down this route, DO NOT simply make pages that are just city and towns for that county with just a bit of content.

Spend time creating each area one by one for your niche and grow the site bit by bit. Low quality content in just a few areas of your site can cause the whole site to struggle.

If done wrong you can damage the site by taking the focus and theme of the main services being provided.

Do you have a Manual Penalty? How have you confirmed you have the penalty? Is there an option to send a reconsideration request in Web Master Tools?

Removing those links is always the best thing to do. However I would start by putting them all in a disavow file first so that Google can start to ignore them as dofollow links. Meanwhile you can start to remove them.

However if you have a Manual penalty, you will have a lot more work to do. Let me know and I will guide you.

I have used them ALL over the years.

It all depends on what you are trying to achieve? What do you want as an end result by doing this?

You might be better of spending your money/efforts on brand marketing or an actual PR agency, nobody in the press is interesting in Press Releases from most PR sites. You want to get a few good pieces of news out to some great sites that target your key market.

Also be careful with PR sites, Google recently unleashed and attack on them and anyone using them, if you do a press release don't put a link on it. NOT even a url or a text url that has no link, many syndicated sites turn text url's in to actual url's. (its a ridiculous situation) and you could get a penalty on your site for it.

hmmm.. seems like Google is getting some strong linking signals that this is the popular page to arrive at.

The canonical tag on the homepage is the right way to go.

You could 301 redirect any customer that lands on you with an affiliate code in the url? This would be a very simple bit of code you could even put it in an an include at the top of each page. This way those pages never even exist and you get all the link juice.

One other thing might be to put a noindex on any page that has an affiliate parameter. But you would lose the link juice.

You have done the right thing using the canonical tag, I presume if a mobile user goes to one of your pages they will be redirected to a mobile page?

If so I see little advantage in having the page indexed. For the safety of your site with regards to Panda I would noindex those pages.

Google have said there is no penalty for internal duplicate content but it is what they don't say that is the problem. There is an algorithmic devaluation and you don't want the hassle.

Without knowing a lot more....

The current state of Google would suggest you keep both sites. Do you interlink them? If so DON'T.

It is easier to rank for niche results with a niche site, however you will have a more powerful site overall with once main site that you can focus all your time on.

Is it possible to rewrite the product descriptions for one of the sites? This make the site more powerful and independent from the other?

Anyone at Google would say combine them, but a penalty is just one small mistake away from you having no business over night. Keep them both (re-write the content)

The fact that you have higher conversion rates on the niche show you that it is easier to rank and easier to show your customers you are an expert in the field. I would not mess with that.

There is a great article on this site about it

http://moz.com/blog/keyword-volume-tools