Here's an overview of where you may find the different logfiles and how you enable debug or start up using command line switches for our windows applicaitons.
Enable debug log (Win)
SOUser.ini Used by SOCRM.exe, SOAdmin.exe and ReporterStudio.exe
SuperOffice.config Used by SOCRM.exe, SOAdmin.exe and ReporterStudio.exe
Command line switches for SOCRM.exe, SOAdmin.exe
Enable debug log (Web)
Web.config
Web Tools Diagnostics
Enable debug for Outlook Mail Link
Enable debug for Notes Mail Link
Enable debug for Ribbons
Service log files
Service config
Debug service tasks failing or not running