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Would you worry about it if the categories are somewhat useful for users to drill down the content?

For example:
/product.html
/aluminum-baseball-bats/product.html
/little-league-baseball-bats/product.html

They don't sell bats but it is the easiest way to describe it I guess.  In this cause would you still 301 redirect the two longer urls to /product.html

Thanks that is what I was thinking, I just need to know more about if the bots will follow the canonical's past one level when pointing to a different domain and if so how many levels on the different sites.

Interesting idea, I might have to do that.  Right now I have canonical elements on the .com

It is a magento store so it creates dirty duplicate content when the products are in different categories out of the box, for example magento creates the following product pages:

domain.com/store/productcategory1/product.html
domain.com/store/productcategory2/product.html
domain.com/store/product.html

In this case I have canonical elements pointing the categories to the main root domain.com/store/product.html

So you think it would be better to do a 301 redirect for the different product urls that are in subcategories?

We are fighting some duplicate content issues across multiple domains. We have a few magento stores that have different country codes. For example: domain.com and domain.ca, domain.com is the "main" domain.

We have set up different rel="alternative codes like:

The question is, do we need to add custom rel="canonical" tags to domain.ca that points to domain.com?

For example for domain.ca/product.html to point to:

Also how far does rel="canonical" follow?  For example if we have:
domain.ca/sub/product.html canonical to domain.com/sub/product.html
then,
domain.com/sub/product.html canonical to domain.com/product.html

+1 for Raven Tools.

I have used the Raven Tools plugin before, sometimes I find myself just getting under the hood and coding out some of the markup myself.  Just to make sure I have all of the information I want and need, in the most recent format.

Thanks a ton.  I do have one last question, well for know.  I am not sure about the etiquette for Moz, so I don't know if I should ask it here.  But I will anyway, live and learn.

Let's say I have a site with domain.com and a store on subdomain.domain.com
We want to link the main\subdomain back and fourth.  Would this be a valid thing to do in the navigation since the point is to get the customer to the store?  Or, do the spiders view subdomains as separate entities? I would rather put the store under a directory but it is hosted by a third party.

I have read the following but I don't know the validity, "Each subdomain is considered a separate site for SEO and rankings. But links to within site sub domains are considered as internal links by Google."

I assume if that is true, I have nothing to worry about with concerns of nofollow on those links.

So essentially, avoid, and remove, repetitive links that are found across sites in the header\footer\sidebar areas and focus on getting, or placing, fewer links in relative content.

Correct?

I have a question with the penguin update. I know they are really cracking down on "spam" links.  I know that they are wanting you to shift from linking keywords to the brand name, unless it makes sense in a sentence.

We have five sites for one company in the header they have little flag images, that link to different country domains.  These domains all have relatively the same domain name besides the country code.  My question is, linking these sites back and fourth to each other in this way, does it hurt you in penguin?  I know they are wanting you to push your identity but does this cross-site scheme hurt you?

In the header of these sites we have something like this.

I am assuming the best strategy would probably be to treat them like separate entities. Or, just focus on one domain.

They also have some sites that have links in the footer but they are set up like:
For product visit Domain.com

Should nofollows be added on these footer links as well?  I am not sure if penguin finds them spammy too.