Quick clarification point to prevent confusion:
- MSMQ 5.0 means Windows 7 and Windows Server 2008 R2
- MSMQ 4.0 means Windows Vista and Windows Server 2008 'R1'
Currently there doesn't seem to be much to worry about - business as usual for most customer.
- SHA 2 Is the Default Hash Algorithm
This will affect all MSMQ systems that use message authentication. Machines running MSMQ 4.0 and below are expecting to use Secure Hash Algorithm 1.0 (SHA-1) by default and will be unable to exchange signed messages with those running MSMQ 5.0. You can enable support for a lower encryption algorithm (SHA1, Message Digest version 2 (MD2), MD4, MD5, and Message Authentication Code (MAC)) with the new WeakHashAlgorithms registry value.
- Removal of Windows 2000 (a.k.a. Down-level) Client Support Service
This will affect Windows 2000 machines running MSMQ 2.0 in Active Directory-integrated mode (as opposed to Workgroup mode). If all the domain controllers have been upgraded to Windows Server 2008 R2 then MSMQ 2.0 clients will be unable to contact them. Applications will probably encounter problems, depending on what they are coded to do - public queues may be unavailable, for example. Workaround for this is to leave some older domain controllers around for the MSMQ clients to contact. Remember that MSMQ works on site boundaries so it will not be enough to have these older DCs in the same domain - they need to also be in the same logical site, which may be a problem for customers with a one-site-per-branch configuration.
Note - Windows 2000 leaves extended support on July 13th, 2010, ten years after it was released, as documented on the Microsoft Product Lifecycle website.
The "What's New" article also mentions "Ability to Handle a Large Number of Queues" but that's just an optimisation rather than new functionality. There will have been a number of other changes to improve performance - this one was just more noteworthy than the rest.