<p>I'm setting up a solution to deploy, driven by a batch file so it's reproducible 
- I've got a binding file that works but I've now added on my MSMQ adapters
- works on my local machine, but I've found I have to add a userid and password to get it to work on the actual server
   - it's in the domain, my virtual dev machine is just workgroup</p>

<p>Is there someway to add the userid and password to the file ?
  - seems unlikely as that'd have the password in clear text, but what's the solution
  - I sort of think something w.r.t. SSO, but that is an area I've not been near </p>

For security reasons, when you export
  bindings, BizTalk Server removes the
  passwords for the bindings from the
  file. After importing the bindings,
  you must reconfigure passwords for
  send ports and receive locations
  before they will function. You
  configure passwords in the Transport
  Properties dialog box of the BizTalk
  Server Administration console for the
  send port or receive location. For
  instructions, see How to Create a Send
  Port. See also How to Create a Receive
  Location.
From
http://msdn.microsoft.com/en-us/library/aa558708.aspx
If you however open the biding file and scroll down to the line with the properties for the MSMQ Adapter you'll find the empty nodes. All you then have to do is to fill these out and the right values and they will be used the next time you import the binding file.
Of course you'll have to remember to redo this every time you export a new binding ...