This sample built for the Biztalk 2006 Design Contest shows how a per-instance custom pipeline can be used to set the map name in a message. Then, the message can be mapped dynamically using an Orchestration. This allows for a consistence approach to transformation and exceptions. Set up: Just extract to your C:\ drive and follow the instructions in the Word document.
This sample will also work with BizTalk 2006 and BizTalk 2006 R2.
Get more information from the original blog post on this topic: http://www.biztalkgurus.com/blogs/biztalk/archive/2005/09/19/Design-Contest-Entry-_2D00_-Dynamic-Transforms-in-Biztalk-Server-2006.aspx