At this moment, Microsoft has 2 different tools in order to build workflows:
Although they are equal in many aspects, we should consider their differences in order to build our Enterprise Application/Integration and choose the best that fits our needs. Luckily, from now on, we have a resource that should help us with that task.
Kent Brown wrote an article entitled BizTalk Server 2006 or WF? Choosing the Right Workflow Tool for Your Project. I advise you to read it.
Until next time ;)