2: Application layout and architecture -- Microsoft Visio
Let's face it: Applications can get complex today. Virtual machines, replicated databases, firewall configurations, virtual IP addresses, mobile applications, and more make documenting an application flow no easy task. Again, I've found Visio to be the tool that reigns supreme. In this example, many complicated aspects of the infrastructure are represented visually in one flow. While it doesn't address the details of aspects such as the database replication, it is a good springboard to those other areas of key content.