Placing canonical tags isn't an option?  Detect that the page is being viewed through the subdomain, and if so, write the canonical tag on the page back to the root domain?

Or, just place a canonical tag on every page pointing back to the root domain (so the subdomain and root domain pages would both have them).  Apparently, it's ok to have a canonical tag on a page pointing to itself.  I haven't tried this, but if Matt Cutts says it's ok...

I've never used Xenu before, but if you can save the export as a txt file, you can import that into Excel.  Here are some sample directions I found.

Google images can search by image!  Go to images.google.com, and click the little photo icon on the right of the search bar.  You can search by image URL, or upload the image directly to Google to search.

Google just announced some tags to help support pagination better.  They say if you have a view all option that doesn't take too long to load, searchers generally prefer that, so you can rel=canonical to that page.  However, if you don't have a view all page, then you can put these nifty rel="next" and rel="prev" tags in to let Google know your page has pagination, and where the next and previous pages are.

View all: http://googlewebmastercentral.blogspot.com/2011/09/view-all-in-search-results.html

next/prev: http://googlewebmastercentral.blogspot.com/2011/09/pagination-with-relnext-and-relprev.html

Each subdomain may have its own robots.txt file.  So for that subdomain, you can put:

User-agent: *
Disallow: /

In the robots.txt, and that should do it.

Please note that disallowing pages in robots.txt will not necessarily mean they won't appear on search result pages.... if people link to pages that are disallowed on that subdomain, they can still appear in SERPs.  I had this happen with a few pages, which leads to funny listings in the SERPs because Google has to guess what the page title and description of the page should be, since it's not allowed to read the page.  The meta noindex tag is the way to go if you want to be really sure the page doesn't appear in the SERPs.  If you use that, don't disallow the page.  Here's a recent SEOMoz post about it: http://www.seomoz.org/blog/robot-access-indexation-restriction-techniques-avoiding-conflicts

Disallowing in your robots.txt keeps the bots from indexing your pages going forward, but Google may keep returning them in search results.  This post has great explanations about ways to remove pages from indices: http://www.seomoz.org/blog/robot-access-indexation-restriction-techniques-avoiding-conflicts

The surefire way to get them out of the index is to remove the disallow from your robots.txt, and add a meta noindex tags on all the pages you want removed.  Once they're reindexed by Google, they'll no longer appear in SERPs.