A common customer request is for a tool to help guide network designers with their implementation strategies. Network Managers want to see a blueprint for ALL devices and software – both operating system and application layers. That type of help from Microsoft comes in two forms: high-level guidance and product specific guidance.
First, the Windows Server System Reference Architecture (WSSRA) is a detailed reference architecture, tested and proven in labs, that yields valuable implementation guidance for meeting the requirements of an enterprise. Customers can use this guidance to build highly available, secure, scalable, manageable, and reliable enterprise infrastructure. By following the recommendations in the WSSRA documentation, an organization can quickly and efficiently plan, build, and operate an infrastructure to support its long-term business needs.
The Microsoft Technology Blueprint for Primary and Secondary Schools is a high-level blueprint document that aligns educational objectives to the core technology infrastructure that schools require to support these objectives. Although titled for use in K12, I found many of the chapters hold good advice for even higher education institutions. The document also includes links to many case studies.
Still high-level (but product specific) is the Microsoft Exchange Service Management Guide which applies Microsoft Operations Framework (MOF) principles and specific prescriptive guidance for managing Microsoft Exchange in a mission-critical setting. The guidance will help you implement process and team best practices within the context of the MOF Process Model. There are such guides for most of Microsoft's server products. These guides are great for project management, but typically do not cover actual architecture.
For specific how-to architecture the TechNet Library holds a wealth of information. A good search parameter on the TechNet site is “solution accelerators”. Solution Accelerators are created by the Microsoft product groups and can take many forms. For example, the Solution Accelerator for Microsoft Office SharePoint Server includes an External Collaboration Toolkit for SharePoint, How Microsoft Moves ITIL V3 from Concept to Practice, Infrastructure Planning and Design, Microsoft Assessment and Planning, SharePoint Asset Inventory Tool Executive Overview, SharePoint Capacity Planning Tool, SharePoint Monitoring Toolkit Executive Overview and even a link to the Windows Server 2008 Security Guide.