I think the footer is the best way to interlink the websites in a non-obtrusive way for users.  This should make your main corporate site your top linking site to each subdomain - and this is something you should be able to verify in a tool like Google Webmaster Tools.  I do not have any specific examples to support this, but this is a common web practice.

This is not 100% related, but Google recently suggested using Footer links as one way to associate your web content with your Google profile account:

http://www.google.com/support/webmasters/bin/answer.py?hl=en&answer=1408986

So you can figure if Google looks to footer links to associate authorship - they would likely do the same to relate sites together.

Interlinking is definitely a factor - but content is what matters.

Take the Disney brands that live on Go.com:

Espn.go.com

Abc.go.com

Abcnews.go.com

They all live on Go.com but Google surely knows they are really separate sites that cover different topics.  Same for any blogspot.com, typepad.com, etc. hosted blog.  The millions of blogs there cover a wide range of topics and search engines understand that they are not related just because they share the same host domain.

On the other end of the spectrum - if your site just has two subdomains - let's say www.website.com and blog.website.com ... which cover the same topics and link to one another, search engines would more likely associate those two addresses.

Interlinking is definitely a factor - but content is what matters.

Take the Disney brands that live on Go.com:

Espn.go.com

Abc.go.com

Abcnews.go.com

They all live on Go.com but Google surely knows they are really separate sites that cover different topics.  Same for any blogspot.com, typepad.com, etc. hosted blog.  The millions of blogs there cover a wide range of topics and search engines understand that they are not related just because they share the same host domain.

On the other end of the spectrum - if your site just has two subdomains - let's say www.website.com and blog.website.com ... which cover the same topics and link to one another, search engines would more likely associate those two addresses.