Appfabric and BizTalk does some of the same things and if you look at the future for the two products they will melt together in the long term. This presentation from the partner conference this summer tells a little about what is the future for the two
products. A basic answer is that Appfabric is a middleware platform for newer web technologies like Windows Communication Foundation, Windows Workflow Foundation. BizTalk is the integration platform that talks with older technologies and is the proven product
on the block as it has been around in a lot of years where the core engine hasn't changed that much. At this time you might look at Appfabric to do smaller solutions that isn't very mission critical and BizTalk to do the heavy enterprise integration stuff.
Hope this helps you.Torben Christiansen http://snatchedmoments.blogspot.com/