These are the websites mentioned in my TechEd Europe session about Lync & Certificates.
Troubleshooting tools:
Troubleshooting TLS1.2 and Certificate Issue with Microsoft Message Analyzer: A Real World Example
Microsoft Lync Server 2013 Debugging Tools
Msdiagnostics: http://msdn.microsoft.com/en-us/library/gg132374(v=office.12).aspx
Microsoft Remote Connectivity Analyzer: https://testconnectivity.microsoft.com/
Troubleshooting scenario’s:
Fix for an Expired Intermediate SSL Certificate Chain
How to get a Root Certificate update for Windows
Lync Server 2013 Front-End service cannot start in Windows Server 2012
Lync Server Central Management Store replication failures
Understanding and Troubleshooting Microsoft Exchange Server Integration
SSL vulnerability / Poodle: