What are the various scenarios where one would prefer BizTalk Server ? Further which version of BizTalk would you recommend 2006 or 2009 ?
I'd recommend BizTalk over Jitterbit if your team feels at home with the whole ms stack and I'd recommend 2009 over 2006 mostly because of the updated platform support (VS 2008, .NET 3.5, MS SQL 2008, MSBuild).
BizTalk is the right thing if you need the added value of management and monitoring tools. If you just want to build a low level EAI platform BizTalk may be too expensive and you'll do better with a homebrew WCF+WF solution.
I confess I'm biased because I was tied to BizTalk 2002 until just now and am admittedly overwhelmed by the possiblites of BizTalk 2009.
Microsoft has done a great job building a robust and scalable product in BizTalk Server. So it saves you from writing all the plumbing necessary for handling message transfer. It does come at a cost however. Not only must you know .NET (which there are plenty that do), you need experience with XML (as all messages are converter to XML), XSLT (i.e. Maps), and specialist knowledge in the speak and architecture of BizTalk. That knowledge and experience will take time to build. For enterprise class systems where you're pumping lots (or large) messages through at least daily if not in real-time, BizTalk can be a lifesaver.
-Krip