Hi Mark,

I personally would run a clean 301 to the new site, then use something like $_SERVER['HTTP_REFERER'] (in PHP) to determine where the user came from.  If it's from the old site, run a small banner in the header (like Hello bar) to advise your users of the change. This would be a lot cleaner for search engines and very user friendly.

Don't forget to transfer the sites worth using webmasters...

Hope this helps.

Dan