Just downloaded the new version of Microsoft Threat Analysis & Modeling tool to have a quick play with it. Seems like a fairly slick program and walks you through building a comprehensive threat model of an application. Here's the blurb:
Microsoft Threat Analysis & Modeling tool allows non-security subject matter experts to enter already known information including business requirements and application architecture which is then used to produce a feature-rich threat model. Along with automatically identifying threats, the tool can produce valuable security artifacts such as:
- Data access control matrix
- Component access control matrix
- Subject-object matrix
- Data Flow
- Call Flow
- Trust Flow
- Attack Surface
- Focused reports
I managed to build a sample threat tree within a few minutes, but it's quite a job to map all the threats against a particular application (especially an n-tiered one)
Check it out: Download details: Threat Analysis & Modeling v2.0