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Thanks, Charles for taking a moment to comment.  I guess I was just a little unsure about using the canonical on the same page that contains a rel=NOINDEX.  I read that google suggest not placing a canonical on pages with a rel=NOINDEX, NOFOLLOW but could not find anything on using a canonical with simply the NOINDEX tag.

Thanks again!

I have a real estate company: www.company.com with approximately 400 agents.

When an agent gets hired we allow them to pick a URL which we then register and manage. For example: www.AGENT1.com

We then take this agent domain and 301 redirect it to a subdomain of our main site. For example
Agent1.com 301’s to agent1.company.com

We have each page on the agent subdomain canonicled back to the corresponding page on www.company.com
For example: agent1.company.com canonicles to www.company.com

What happened is that google indexed many URLS on the subdomains, and it seemed like Google ignored the canonical in many cases. Although these URLS were being crawled and indexed by google, I never noticed any of them rank in the results.

My theory is that Google crawled the subdomain first, indexed the page, and then later Google crawled the main URL. At that point in time, the two pages actually looked quite different from one another so Google did not recognize/honor the canonical. For example:
Agent1.company.com/category1 gets crawled on day 1
Company.com/category1 gets crawled 5 days later

The content (recently listed properties for sale) on these category pages changes every day. If Google crawled the pages (both the subdomain and the main domain) on the same day, the content on the subdomain and the main domain would look identical. If the urls are crawled on different days, the content will not match.

We had some major issues (duplicate content and site speed) on our www.company.com site that needed immediate attention. We knew we had an issue with the agent subdomains and decided to block the crawling of the subdomains in the robot.txt file until we got the main site “fixed”.

We have seen a small decrease in organic traffic from google to our main site since blocking the crawling of the subdomains. Whereas with Bing our traffic has dropped almost 80%.

After a couple months, we have now got our main site mostly “fixed” and I want to figure out how to handle the subdomains in order to regain the lost organic traffic. My theory is that these subdomains have a some link juice that is basically being wasted with the implementation of the robots.txt file on the subdomains.

Here is my question
If we put a ROBOTS rel=NOINDEX on all pages of the subdomains and leave the canonical (to the corresponding page of the company site) in place on each of those pages, will link juice flow to the canonical version?

Basically I want the link juice from the subdomains to pass to our main site but do not want the pages to be competing for a spot in the search results with our main site.

Another thought I had was to place the NOIndex tag only on the category pages (the ones that seem to change every day) and leave it off the product (property detail pages, pages that rarely ever change).

Thank you in advance for any insight.

Thank you Miriam.  We have switched from one brand to another (EasyStreet to Highgarden) in a couple of our markets.  We implemented a 301 redirect strategy for those sites and saw very little effect on our organic traffic.

Thanks again for your input.

I am a partner in a real estate company that operates in 10 different markets across the country.  Each of these markets has it's own individual domain.  My question is should we consolidate each of these markets into one domain that services all markets?  What would we possibly gain or lose from an organic traffic standpoint?

In some of our more established markets (Indianapolis, Las Vegas, Tampa, Orlando and Charlotte) our organic traffic accounts for 50-60% of our total traffic.  In some of our newer markets (Denver, Phoenix, San Diego) it accounts for less than 15%.

We do operate under two different brand names.  EasyStreet Realty and Highgarden Real Estate. EasyStreet has been around since 2000 with most of our Highgarden sites only up for 6-24 months. Another question is we are considering converting all EasyStreet divisions to Highgarden.  I am a little reluctant to do so, since most of our organic traffic is coming from our EasyStreet sites.  Thoughts?

You can find links to all our sites at www.easystreetrealty.com or www.highgarden.com

Thank you in advance for your insight.

Thanks SeoStallion.

That is how we are handling it currently.

Our corporate site provides MLS data to users, with the end goal of generating leads. Each registered lead is assigned to an agent, essentially in a round robin fashion. However we also give each agent a domain of their choosing that points to our corporate website. The domain can be whatever they want, but upon loading it is immediately directed to a subdomain. For example, www.agentsmith.com would be redirected to agentsmith.corporatedomain.com. Finally, any leads generated from agentsmith.easystreetrealty-indy.com are always assigned to Agent Smith instead of the agent pool (by parsing the current host name). In order to avoid being penalized for duplicate content, any page that is viewed on one of the agent subdomains always has a canonical link pointing to the corporate host name (www.corporatedomain.com). The only content difference between our corporate site and an agent subdomain is the phone number and contact email address where applicable.

Two questions:

1. Can/should we use robots.txt or robot meta tags to tell crawlers to ignore these subdomains, but obviously not the corporate domain?

2. If question 1 is yes, would it be better for SEO to do that, or leave it how it is?