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Since (I assume this is what is happening) your ecommerce platform is duplicating the entire page, code and all, and putting it at these new URLs, having the canonical tag of the original page URL in the code for the right/real page will mean that, when it gets duplicated, the canonical tag will get duplicated as well and point back to the original URL.  Make sense?

Can you talk to your ecommerce platform provider?  This can't be an intended feature!

Oh how frustrating!

There are a couple of things that you can do. Updating your robots.txt is a good start since the next time your site is crawled, Google should find that and drop at least some of the offending pages from the index.  I would also go in to every page of your site and add in a rel=canonical tag to the original version of the URL.  That way, even if your ecommerce platform is generating odd versions of the URL, that canonical tag will be on the duplicate versions letting engines know they're not the original page.

For the existing pages, you could just 301 them all back to the original versions, or add the canonical tag pointing back to the original versions.  I would also add the tag to these pages to let Google know not to include them in the index.

With pagination and canonicalization there are a few different approaches, and each has its pros and cons.  Dr. Pete wrote a really great post on canonicalization that just went out, you can read it here: http://www.seomoz.org/blog/which-page-is-canonical.  I also recommend reading Adam Audette's post on pagination options at Search Engine Land: http://searchengineland.com/the-latest-greatest-on-seo-pagination-114284\. I hope that helps!

I would be cautious with doing too much article marketing - you're at risk that search engines will see your article on multiple sites, deem it duplicate content, and then decide your article on a submission site should rank instead of the version on your own site.  With the Penguin release, Google is also taking a closer look at links from article submission sites - I wouldn't be surprised if those links become lower and lower value as time goes by.

Definitely let Google discover your backlinks on its own - grow your link profile too quickly and they'll take a close look at your site to see if any of those links look suspicious.

There are plenty of more valuable ways to grow your link profile.  Mike King recently had a post on this topic at http://www.seomoz.org/blog/the-noob-guide-to-link-building - I suggest you check it out for new ideas on how to build links to your site.

Right - so you would be using the canonical tag on your clients' site to point to the ezine articles site.  Otherwise it will just end up looking like duplicate content - but again, if you just want to noindex, follow the content then canonicaling won't be an issue.

Recently Google has been taking a closer look at anchor text, because exact keyword anchor text isn't really how "natural" links (i.e. links you didn't build) look.  Ben has a great point that natural link growth usually means anchor text that is either your brand name or your URL.  Rob Kerry recently did a Whiteboard Friday on the Penguin update that may shed some more light on your predicament: http://www.seomoz.org/blog/the-penguin-update-whiteboard-friday

A majority of your inbound links should not have exact keyword match anchor text.  Instead, focus more on building overall link volume, both for your domain and individual pages.  Try to get links from high-authority sites, and create pieces of content that people want to share and link to - these are link building strategies that will be more successful than a hyper-focus on anchor text, whether branded, keyword or "click here."

I think the steps Ben outlines above are a great start.

If you don't want them to appear in the index but still want them on the site for user reasons, noindex, follow is one way to do it - you could also use the rel=canonical tag to call out the original post as the canonical one.

When thinking about links without keyword-rich anchor text, think about how people are linking to you on their own, without your actually building the link.  They're more likely to link either with your main brand name (AccuPOS), your domain name (AccuPOS.com) or text like "read more" "click here" etc.  That's one reason that Penguin has targeted keyword-rich anchor text links, because they aren't "natural" - i.e. it's unlikely someone would link to you with "Restaurant POS Software" unless you specifically ask them to.  So when building links it's helpful to have a good mix of these other less-specific anchor texts, to appear more natural.  If the link appears on a page that is talking about your keyword, there's some evidence to suggest that that semantic info might help in a similar way to keyword-rich anchor text.

In a post-Penguin world, I'd be leery of this kind of automated anchor-text-rich link building.  If you continue with this approach, make sure you're also getting plenty (i.e. a majority) of links without keyword-rich anchor text.  Otherwise, yes, they will both count as they are to different pages.

For the phrase that begins the title tag, I don't think having more terms in the tag is going to affect rankings for that phrase one way or another.  For any additional phrases in the tag, whether or not the page ranks for the phrase is also going to depend on how the phrase is used on-page, but I agree that they usually have diminishing returns rankings-wise.

As for testing one phrase vs. multiple phrases and their effect on CTR and rankings...sounds like a great YOUMoz post to me!

A longer page title is certainly ok - although, as the other answers noted, yours is pretty unreadable by humans.  Too many keywords in a title tag can make your page look "over-optimized" and have a negative effect - not to mention that users are less likely to click on an unattractive tag.  I would advise targeting a maximum of 2 keywords in a title tag.

WIth Google's recent updates it's becoming more important to have a tag that's not TOO long, though.  Title tags longer than about 68 characters (including spaces) may be automatically shortened by Google - or Google may choose to use different text from the page altogether in place of the title tag.  This can make for some pretty weird results since Google's auto-inserted text isn't always as nice of a user experience as your hand-crafted tag.  So make sure your tags are shorter than 68 characters so as not to get truncated.

Adding "noindex" to your page doesn't just keep link juice from flowing to it - it also means that it won't appear in the SERPs at all - what about your users who are actually trying to find your page? I wouldn't noindex anything unless you're sure that you don't want anyone to be able to find that page via organic search.

When you're structuring your site, it's better to focus on having a structure that allows search engines to crawl and find every page (no orphan pages, no content that search engines can't crawl, no duplicate content) and that allows users (you know, the people who give you money!) to easily find content.  If you want to conserve link juice on your pages, try to make sure you don't have a ton of links on every page, but don't try to nofollow/noindex content based solely on the idea of link juice - it won't work.

Hi - I didn't see the drop-down window called "popular products" on your page so it looks like you've decided to remove it.

I think a "popular products" section can be valuable for users.  If you do decide you want to direct users to your most popular products in the navigation or on the home page, doing so shouldn't give you too much of a hit - although I agree that creating short articles about them just for SEO purposes is probably something you want to stop doing.

After Panda/Penguin, it's unlikely that having a ton of keyword-anchor-text-rich links from one page on your site to another page on your site will do much good, so if your users aren't really using them to travel from page to page, I'd remove them (which it looks like you did).  If your pages didn't take a rankings hit after you removed them,  you're probably fine.  Let me know how it went!

One of the questions Google is trying to answer with fresh content is "is this site still relevant?"  If you're not updating your home page regularly because it's not necessary for your users, continuing to get new fresh links is a great way to keep sending the signal that your page is still relevant.

I would definitely advise against making a bunch of random changes to your home page just for Google's benefit - but if there are ways you can include more fresh or dynamic content that would also be good for users, that might be something to explore.  Maybe have a link to your newest or most popular blog post that updates when you post?