A couple of posts back, I described an issue we had with emails not being downloaded by the BizTalk POP3 adapter. I'm happy to say that after working with Microsoft, a hotfix has been created for this which I tested yesterday. It'll take a few weeks for the KB article to be written up but I'll post details as soon as I have them. This fixes the "The POP3 adapter received a response line from a server that contains more than 512 characters" issue.
EDIT... some good news. It looks like the fix will find its way into BTS 2006 R2 SP1. The KB number will be 975826
EDIT 2: Here's the kb link: http://support.microsoft.com/kb/975826/en-us