Introduction
When I started studying Windows Workflow Foundation (WF), I was confused with the fact that there are lots of similarities between WF and BizTalk Server. Then I did some more studies and got hold of some good posts from Microsoft regarding the comparison of WF and BizTalk Server. Let me share what I summed up. 
Windows Workflow Foundation
Windows Workflow Foundation (WF) is a programming model, set of tools, and runtime environment that allows one to write declarative workflows on the Windows platform to represent the execution model of your programs. The WF runtime is part of the .NET Framework, first appearing in .NET Framework 3.0, with improvements in .NET Framework 3.5. 
Microsoft BizTalk Server
Microsoft BizTalk Server provides an efficient and effective way to integrate systems and businesses through manageable business processes, enabling them to automate and orchestrate interactions in a highly flexible and highly automated manner.
 Microsoft BizTalk Server provides a development and run-time environment for business process management (BPM) and automation. 
Fundamental Difference between WF and BizTalk Server
WF and BizTalk are not competing technologies. Windows Workflow Foundation and BizTalk are complementary technologies that serve different needs. 
|      Windows    Workflow Foundation   |          BizTalk    Server  |    
|     WF   is a developer framework used to implement workflow inside an application.   |        BizTalk   Server is a product that can be used to implement workflow across disparate   applications.   |   
|     WF   is a framework that provides the building blocks needed to build   workflow-based applications.   |        BizTalk   is an integration server that includes the ability to add business process   automation.   |   
|     WF   is a framework that provides developers with the base components they need to   build the modules that will be used to automate processes.   |        BizTalk   Server is a platform that provides developers with the pieces they need to   automate business process.   |   
|     WF   does not have the inherent features or tools for tracking, administration and   so on that is available with BizTalk.   |        BizTalk   provides a lot of capabilities that are needed for serious business process   automation that WF developers would have to write. To name a few, BizTalk has   proven scalability, tracking, administration and transformation capabilities   that a WF developer would need to write from scratch.   |   
Comparison between WF and BizTalk Server
The following table shows the feature comparison between WF and BizTalk Server: 
|      Feature      |          Windows    Workflow Foundation   |          BizTalk    Server   |    
|     Hosting     |        Hosted   in a custom application (client-side execution, but the client could be an   ASP.NET application)   |        Server-side   in the BizTalk process   |   
|     Designer     |        Included   in Visual Studio, or custom designers can be written   |        Included   in Visual Studio   |   
|     Scalability     |        Developer   must implement   |        Well-proven,   highly scalable   |   
|     Transactional   integrity   |        Developer   must implement   |        Long   running and atomic (ACID) transactions   |   
|     Tracking   infrastructure   |        Simple   framework pieces provided that allow you to build the tracking infrastructure     |        Comprehensive   Business Activity Monitoring infrastructure provided   |   
|     Runtime   modification of “in-flight” workflows   |        Yes,   but developer must implement   |        No,   workflows are defined at design time   |   
|     Cross-platform   integration capabilities   |        Not   supported natively   |        Extensive   adapters available   |   
|     Composability     |        WF   processes cannot directly invoke a BizTalk application, although you could   indirectly by calling an orchestration that had been exposed as a Web service   (for example), or perhaps by API usage   |        A   BizTalk process could invoke a WF process via Web service call, or from a   helper class or expression shape   |   
|     Management   and administration   |        Developer   must implement   |        Extensive   set of tools provided for IT pros to administer and track execution   |   
|     Windows   Communications Framework (formerly “Indigo”) support   |        Natively   supported   |        Through   an adapter, or could be called from an expression shape or helper class   |   
|     Rules   engine support   |        Yes     |        Yes     |   
|     Extensible   activities   |        Yes     |        No     |   
|     Transformation   capabilities   |        No     |        Yes     |   
|     Programmability     |        WF   is a framework. You must implement applications to use it.   |        BizTalk   Server exposes APIs for most parts, and has numerous extensibility points   such as pipeline components, adapters and “functoids” (out-of-the   box and custom mapper components)   |   
Very helpful, but BizTalk server column was partially cut. I tested in chrome, IE too.
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