The service pack is available now from the Microsoft Download Centre.

There's a list of fixes included in BizTalk 2006 R2 SP1 at the Biztalk Customer Response Team's blog and in the Knowledgebase.

Here's the blurb: 

SP1 includes a roll-up of hotfixes from the BizTalk Server 2006 and 2006 R2 releases, some hotfixes from the BizTalk Server 2009 release, as well as some additional enhancements. Some of the key fixes and enhancements in this service pack are the following:

New Features

  • For WCF-Custom and WCF-CustomIsolated Adapters, the ability to look up custom bindings from locations other than machine.config. 
  • Support for using multiple certificates to sign outgoing AS2 messages

Better reliability, performance, and scale for the following key features

  • Throttling and dehydration of orchestrations.
  • Archiving and purging operations.
  • BAM alerts and archiving.
  • HIPAA.
  • Reduced memory consumption in scenarios using scripting functoids.
  • Improvement in the bts_FindSubscription stored proc, resulting in faster execution and lower CPU utilization.

Better management and deployment experiences

  • Performance and user experience improvements of key scenarios.
  • WCF configuration management.
  • Significant improvement in deployment time for send ports using a map.

Improved support

  • X12 and EDIFACT updates.
  • Increased footprint of supported FTP servers and locale.
  • XMLDocument message types in orchestrations.
  • Configurable timeout for Basic HTTP.
  • WCF adaptor now suspends messages instead of terminating when the host instance is stopped.
  • Configurable transaction timeout for WCF Adaptors.
  • Mapping of inline schema for SQL Adaptor now allows for using $ characters as part of the updategram.
  • The SQL Adaptor now supports calling from a BizTalk Server dynamic send port. The following properties can be set on the call to the dynamic port:
          Connection string (all the SQL connection properties)
          Document Target Namespace
          Response Document Root Element
  • Ability to disable generation of Routing Failure Report.
  • Fixes to some issues that used to cause high CPU usage by BizTalk Server hosts due to certain .NET updates.
  • Ability to use multiple certificates for signing outbound messages.
  • Message Pack 2009.
  • Message property tracking with BAM for all messages in the interchange, irrespective of the usage of pipeline or mapping.
  • Integrated tracing to help in debugging EDI specific issues. This improvement is aimed at reducing the time taken for diagnosing and isolating an EDI problem.