Common question we get about stop/start services and wanted to share with the community.  This is what I use and you can modify as you see fit.

##STOP
## "Microsoft Monitoring agent" Workflow Engine
Net stop HealthService              
## "System center management configuration service"
Net stop OMCFG                 
##  "System Center Data Access Service" service" Console/db connection
Net stop OMSDK 
## "SQL Server Services" if needed
Net stop MSSQLserver


##CleanUp
##Delete all files in Health Service
Remove-Item C:\Program Files\Microsoft System Center 2012\Service Manager\Health Service State\* -recurse

##START
##  "System Center Data Access Service" Console/db Connection
Net start OMSDK
## "System center Management Configuration Service" workflows
Net start OMCFG
##  "Microsoft Monitoring Agent" Workflow engine
Net start HealthService
##  start SQLServer if off
Net start MSSQLserver