A while back I wrote a couple of posts about Testing maps in BizTalk. They are at the following links:
BizTalk 2006 R2
http://geekswithblogs.net/michaelstephenson/archive/2008/03/30/120851.aspx
BizTalk 2009
http://geekswithblogs.net/michaelstephenson/archive/2008/12/12/127826.aspx
One possible extension to this might be if you have a map which rather than using the map designer imports a custom XSLT to perform the mapping. (If you are not familiar with this refer to MSDN).
So if you have a custom XSLT then you really have a couple of choices with regard to testing it. The first choice is that you can just run the testing approaches which are described above, or you could also test the XSLT before you use it in the BizTalk map or do both.
If you wish to test the XSLT in isolation you can use the XslCompiledTransform class within the System.Xml.Xsl namespace. This will allow you to load the xsl and then transform an input file to an output file like in the below example. You could then perform a binary comparison on the output file against what it is expected to look like.
Summary
So you can see above this is easy to do. I would probably in practice do 1 test which would test the BizTalk map to ensure it works correctly when loading the custom XSLT and the rest of my tests will focus on testing the XSLT in isolation and testing different cases within the map.