Move it:
MSIT group has just released a whitepaper on moving from BizTalk 2004 2002 & 2004 to BizTalk 2004 2006. It goes into quite a bit more technical detail than our typical case study particularly in regards to their consolidation onto 64bit hardware.
http://www.microsoft.com/technet/itsolutions/msit/deploy/biztlk06upgtwp.mspx