OK... thank you.

If I owned a company that did plumbing, electrical and air I would call it EgolServices.com and I would have ONE website.

All of the links that any part of that business earned would benefit the entire domain.

And all of the trust that my plumbing staff earned would generate repeat business when the same client needed air.  All of the trust that my electric staff earns would generate repeat business for my plumbers.

Why make clients make separate decisions when you are out there doing good work?

The big air conditioner that you want in the house will probably need a more substantial wiring.   Just call EgolServices and they will take care of it.

I think that this is a nobrainer.  NoBrainer.

I would spend the time needed to do an assessment of these pages.

** how many of them have external links

** how many of them pull traffic from search or other sites

** how many of them are currently useful (are people looking at them)

I would delete (and redirect the URL) of any page that answers "no" to the three items above.  These are "dead weight" on your site.

Also, if these are .pdfs of print ads then they might simply be images in a pdf.  (test this by searching for an exact phrase from one of them in quotes and include site:yourdomain.com in the query.   Keep in mind that google can read the text in some images embedded in pdfs.

I had a lot of pdfs with images on one of my site and got hit with a panda problem.  I think that Google thought that the .pdfs were thin content.  So I used rel=canonical to assign them to the most relevant page using .htaccess.  The panda problem was solved after a couple of months.

Also, keep in mind that .pdfs can be used for conversions.  You can embed "add to cart" buttons and links into them and they will function just as on a web page.

If any of these pdfs are pulling in tons I traffic I would figure out how I can put the pdf to better use or create webpage (and redirect the pdf) to best monetize/convert or whatever you business goals dictate.

Can a bot navigate via a back button?

I don't think so.  They can follow links but they can't "click".

I see 6000 pdfs as an amazing opportunity.  Get links on those pages and it will funnel a lot of power through your site.

If that was my site, we would be on that job immediately.  Could be a huge gain for some easy work.

Go back and rework our .pdfs so they at least contain a link back to the homepage?

Yes!  Absolutely!  And, link them to other relevant pages.  If  these are reference documents they could be pulling in a lot of links and traffic from other sites.

In addition toAs well as configure the hyperlinks so they open in the same window instead of a new one?

In my opinion, this is not an SEO issue.  This is a usability issue.   I would have them open in the same window so the back button is available.

.pdf documents are crawled by bots and they accumulate pagerank just like .html pages.

You can include links in them to other documents on the web and bots will crawl those links and pagerank will flow through them.

.pdf documents can be given a "title tag" equivalent by opening their properties and giving the document a title.  This title will display in the SERPs.  .pfd documents can be hard to beat in the SERPs if they are optimized and have links from a competitive number of other web documents.

Lots of document formats behave this way.  Excel, PowerPoint, Word for example.

In my opinion, .pdf documents can trigger a Panda problem for your site if you have a lot of them with trivial or duplicate content (as in print versions of web documents).  They can be given rel=canonical through .htaccess to solve the Panda problem but Google often takes a long long time (sometimes months) to recognize the canonical and use that instruction.