So what about BizTalk and Windows Workflow Foundation? Did you bet on the wrong horse by choosing BizTalk Server? No you didn’t. BizTalk Server is, was, and will be the right architecture for business process and integration on Windows. To properly serve the needs of business process and integration you need a "man in the middle" server that adapts, routes, tracks, manages, scales and has all the appropriate BPM capabilities such as BAM. Windows Workflow Foundation gives you none of that. On the other hand there are many scenarios that Windows Workflow Foundation is useful outside of business process and integration such include page-flow in ASP.NET web applications, workflow within line of business applications that ISVs build, workflow within Office. By targeting ISVs primarily the Windows Workflow Foundation technology can be embedded within these applications.
A. Workflow within applications = Windows Workflow Foundation< BR > B. Workflow across applications = BizTalk Server
Source: What about BizTalk Indeed?