I bumped through this blog entry from one of Rod Trent 's entry and I find it extremely helpful one as well
In Summary what we need to consider would be:
i) OpsMgr Server
“\Program Files\System Center Operations Manager\…\Health Service State” and all sub-directories
“%windir\temp%‟ or other directory depends on the directory store for the ETL files (defined in
starttracing.cmd)
ii) Monitored Server
“\Program Files\System Center Operations Manager\…\Health Service State” and all sub-directories
“%windir\temp%‟ or other directory depends on the directory store for the ETL files (defined in
starttracing.cmd)
iii) DB Server
File path which stores the OpsMgr DB, DW and if applicable ACS DB
iv) OpsMgr Console
\Documents and Settings\
v) Others
%installdir%\Health Service State
%installdir%\Config Service State
%installdir%\SDK Service State
%installdir%\tools\tmf
%windir%\temp\OpsMgrTrace
You will also need to consider to exclude the process of monitoringhost.exe
As for file type exclusion, you will need to consider EDB, CHK and LOG filetypes